Moore's Owls were just not at it in the first 45 minutes at the club he used to manage before jumping ship, and although they did not deserve it, they brought Rovers' 1-0 first-half lead on themselves.
But substitute Callum Paterson's persistence brought him a first goal in 22 appearances, and the other men Moore introduced from the bench, Lewis Gibson and Saido Berahino, combined to put them in front. It was only the striker's third game for the club.
Barry Bannan shook off a saved penalty to crown the 3-1 win.
A less decent man than Moore would have smuggly lapped it up. Moore settled for a restrained wave when the 4,000 away fans asked for one.
Much of what was shouted at him over the 90 minutes was far less cordial. Most of the chants directed towards him were not "Good luck Darren Moore" , but the last 14 letters were the same.
When Dan Gardner put Rovers in front from a 45th-minute penalty it looked like Moore's return might be a much more miserable one.
This always threatened to be a game of "first goal the winner" with Doncaster not having won a league match they conceded first in since shortly after Moore left the club last March, but the Owls not having done so since Birmingham City in February 2016.
That sorry statistic has been put to bed and although Wednesday are no hiugher up the table, they are only outside the play-offs on goal difference now.
Desperately lacking a convincing centre-forward with Nathaniel Mendez-Laing - himself an out-of-position winger - the latest addition to their injury list, Wednesday played most of the first-half football but Doncaster scored the goal.
The Owls saw 68 per cent of the ball in the opening 45 minutes (both halves actually) but Doncaster created just as many chances and put twice as many of them on target. The second of them, from Gardner, was an emphatic penalty with half-time approaching.
Until then, Bannan had seen far too much of the ball for Rovers' liking but when he passes had found their man, he usually wasted it. Neither Florian Kamberi nor Sylla Sow, leading the line together with Callum Paterson on the bench after 21 goal-free appearances, could make the ball stick.
The Scotland international, who had shot over from Kamberi's fifth-minute lay-off, played an excellent ball over the top in the 13th minute but Marvin Johnson's touch took it out of play. His next pass to Sow was wasted by the striker, another to Jack Hunt overhit.
Doncaster's day looked as if it had taken a turn for the worse midway through the first half when the influential Tommy Rowe went off injured but his replacement Josh Martin was straight into the game, touching the ball a couple of times in the build up to a move which ended with his long-range shot, albeit a comfortable one for Bailey Peacock-Farrell to deal with.
That apart, Doncaster's rare spells of possession were fizzling out the same way as Wednesday's.
The Owls' first effort on target was barely worthy of the name, so tame was Sow's header from a Bannan cross after 26 minutes
Then from nowhere, Kyle Knoyle got into the Owls area after 45 minutes and Massimo Luongo brought him down. Gardner hammered the penalty into the roof of the net.
Wednesday might have responded immediately, Jonathan Mitchell tipping Bannan's corner onto the crossbar at the end where he was beaten by a Mickel Miller flag kick weeks earlier.
Moore acted, bringing Paterson and Saido Berahino on at the interval and the ball started sticking more.
But Bannan headed over at a corner and should have been made to pay for it when one centre-back, Ro-Shaun Williams, crossed for another. With Peacock-Farrell rushing out, Joe Olowu missed the target from inside the six-yard box. It would be a costly miss.
The Owls kept battering away, Berahino's shot deflecting into the side netting, Paterson's header from Marvin Johnson's cross ruffling the roof of the net and Bannan shooting just wide before they finally made their breakthrough.
It owed everything to Paterson's persistence, hanging in the air to head in a 71st-minute cross and reacting firstr when it was bundled away. Fans and a blue flare came onto the pitch.
From there, Doncaster crumbled as they too often do.
Williams was extremely unlucky to concede a penalty when the ball was hammered at him but Mitchell dived left and saved Bannan's penalty down the middle with his right foot.
The visitors, though, were not to be denied, recently-introduced centre-back Gibson getting to the byline and pulling a ball back which Berahino controlled, spun on and converted.
Minutes later Johnson broke away and shrewdly waited for Bannan to catch up before allowing him to atone for his penalty miss.
Doncaster Rovers: Mitchell; Younger, Williams, Olowu; Knoyle, Smith, Gardner, Jackson; Griffiths (Agard 81), Rowe (Martin 23); Odubeko (Dodoo 81).
Unused substitutes: Jones, Clayton, Horton, Hasani.
Sheffield Wednesday: Peacock-Farrell; Brennan (Gibson 71), Storey, Palmer; Hunt, Luongo, Byers, Johnson; Bannan; Kamberi (Berahino 46), Sow (Paterson 46).
Unused substitutes: Wildsmith, Agbontohoma, Brown, Waldock.
Referee: C Hicks (Surrey).