The champions leapfrogged Hull into fourth but were far from convincing and forward Greg Eastwood suffered a leg injury that will rule him out of Friday's trip to Hull KR.
"I thought they (St Helens) did well," said McClennan after the visitors lost half-back pairing Kyle Eastmond and Leon Pryce. "To lose your strike pivots, they did really well. We got the points but we're not kidding ourselves that we played great. We did enough to win the game."
While the Saints have a number of injuries, Leeds also have seven first-team players on the sidelines, but have managed to beat Warrington and St Helens in successive weeks with under-strength sides.
McClennan is hopeful that some of his charges will return over the coming weeks, though, and with it he wants to see a return to the form that has seen them win three successive titles.
"We're trying to get some momentum now, if we can pick up the points that's good, but we need to keep improving a lot more and we need to do a lot better," he said.
"I think a lot of clubs have had their injuries and it's made it a challenging season. For ourselves, we've had more players out than people realise, but we've got some coming back soon and that will help.
"The pleasing thing is the 17 that represented the club did their jobs. Can we do better? Damn right. I want to see some more signs that we can go on and win the thing."
Opposite number Mick Potter acknowledged that his St Helens players had faced a task that was "a little bit too tough" as they squandered an eight-point lead.
Already missing seven first-team players, Potter's men had opened a 24-16 but were hamstrung by the loss of Eastmond and Pryce.
Back after four games out with an ankle injury, Eastmond failed to return for the second half after suffering a recurrence of the problem after 20 minutes, while Pryce was led from the field after his back went into spasm.
With young forward Andrew Dixon also off with a groin injury, the Saints ran out of bodies and Leeds showed their class as tries from McGuire and Ryan Hall saw them over the line.
"We lost a couple of players and that made it even harder," said Potter. "We didn't need it, but that's the way it goes sometimes.
"Andrew Dixon picked up a groin injury, Kyle got a recurrence of the ankle and there was a back spasm for Leon – he just couldn't move.
"I think when you lose key players it is difficult to mix and match. I thought they tried as hard as they could but it was just a little but too tough."
England scrum-half Eastmond spent large parts of the second-half trying to shake the injury off by running down the touchline but was unable to do so, although his coach is hopeful he is not set for another lengthy absence.
He added: "We're not sure on Kyle, he could be a couple of weeks. The physio says it's not as bad. We were hopeful he could go back on but it just wasn't right."
Potter also pledged to speak to referee's chief Stuart Cummings about video referee Thierry Alibert's decision to award Hall's match-winning try.
There was some doubt as to whether or not McGuire had got the narrowest of forward touches to the ball as it made its way through to Danny Buderus, with numerous replays proving to be inconclusive.
"I did have a couple of issues with it," Potter said. "I'll have to take it up with Stuart as I thought there was a touch with the ball going forward and an obstruction."
Those two tries midway through the second half from McGuire and Hall helped Leeds move above Hull into fourth after the visitors had been in the driving seat at 24-16 with 17 minutes remaining.
The Saints had got off to the perfect start, scoring after just two minutes.
Scott Donald's failure to hold Pryce's kick gave them a repeat set of six and Donald shelled another kick, allowing Chris Flannery to snap up the loose ball and score. Jonny Lomax kicked the goal and could have added a try moments later, only for Hall to drag him out of play.
Leeds took over and captain Kevin Sinfield produced a kicking master-class to help them score three quick tries and put 10 points of daylight between the two sides.
Sinfield's 10th-minute kick put Ade Gardner under pressure he was unable to handle and Chris Clarkson swooped to score, before another kick from Sinfield forced another error from Gardner and Brett Delaney grabbed his ninth try of the campaign.
St Helens had barely put a foot wrong but were still behind and quickly found themselves with a greater deficit to wipe out as Sinfield's kick bounced wickedly in front of Paul Wellens and into the hands of Greg Eastwood, who started a move that ended in McGuire bouncing over the line.
Carl Ablett's careless handling close to the line cost the Rhinos a fourth try and St Helens made them pay by scoring twice in quick succession before the half-time hooter.
Lomax jinked in at the corner after being played in by Pryce and Matt Gidley, before James Roby's snappy offload sent Flannery pounding 40 metres to the posts for a 10th try of the year.
Chris Dean looked to have continued their momentum two minutes into the second half when he went over, only for referee Silverwood to call a forward pass against Wellens.
Bryn Hargreaves then incorrectly chose to go it alone rather than feed Gidley as Saints increased the pressure on the Leeds line, and that eventually bore fruit as they regained the lead after 52 minutes.
James Graham and Scott Moore sent Pryce through for a fourth try in as many games but Pryce joined Eastmond on the touchline after a collision with Danny Buderus.
Lomax kicked a penalty after Bailey was penalised for an off-the-ball altercation with Roby but the Leeds player made amends when he darted through the line to send in McGuire.
Saints were out of answers without the midfield leadership of Pryce and fell behind.
Bailey offloaded out of a tackle, and, although video referee Thierry Alibert had a long look to see if McGuire's fingertips had touched the ball in transit, play was allowed to continue and Buderus fed Hall, who crossed in the corner for the match-winning try.
Leeds Rhinos: Smith, Donald, Delaney, Senior, Hall, Sinfield, McGuire, Bailey, Buderus, Peacock, Jones-Buchanan, Ablett, Clarkson. Replacements: McShane, Kirke, Ambler, Eastwood.
St Helens: Wellens, Lomax, Gidley, Flannery, Gardner, Pryce, Eastmond, Graham, Roby, Hargreaves, Clough, Dixon, Moore. Replacements: Dean, Fozzard, Ashurst, Emmitt.
Referee: R Silverwood (Dewsbury).
Hero: Danny McGuire
Scored his 16th and 17th tries of the season in helping the under-strength Rhinos move up into fourth place in the Super League table with victory against the similarly weakened Saints.
Villain: Ade Gardner
The St Helens back was obviously targeted as a weak link by Rhinos' Kevin Sinfield and was unable to handle the pressure placed on him by the Leeds captain's kicking master-class.
Both clubs have soldiered on with key players missing so Warrington and Wigan Warriors had better watch out when these two giants are back to full strength at the critical stage of the season. It would be foolish to bet against another Super League Grand Final between Leeds and St Helens.
Key moment: 67th minute
Ryan Hall crosses in the corner for a match-clinching try which is allowed after the video judge rules that Danny McGuire had not knocked the ball forward.
Super League: Hull Kingston Rovers v Leeds Rhinos, Friday, 8.0pm.
Quote of the day
The pleasing thing is the 17 that represented the club did their jobs. Can we do better? Damn right.
Leeds coach Brian McClennan's assessment of his wounded Rhinos.