Marlon King succeeded where Leroy Lita failed – from the penalty spot – to give Coventry victory at the Ricoh Arena.
King struck from 12 yards 12 minutes from time to make Tony Mowbray's team pay after Lita's spot-kick on the half hour had been saved by Keiren Westwood.
Coventry boss Aidy Boothroyd praised his side for grinding out the scrappy victory and leave the Sky Blues in the play-off picture.
Boothroyd said: "We have got players in the team who no matter how we play will create and score goals and that is what the story is about today.
"We ground out a result and we are difficult to beat.
"It's three points, the result is the be all and end all but as coaches we are looking for a little bit more.
"Their penalty came from a counter-attack which is something I think our centre-backs can learn lessons from but Keiren Westwood's saves were outstanding and that's what he can do, he does that in training all the time and we are thrilled that he kept us in it.
"You have to get on with it and stay focused – which we did."
Boro counterpart Tony Mowbray again felt his side's lack of cutting edge proved decisive as they slipped to another defeat.
He said: "We missed a penalty and they scored a penalty. I thought we controlled the game reasonably well after the first 20 minutes where they had a number of free-kick and crosses into the box. We didn't really feel threatened, particularly in the second half.
"We are very disappointed to lose a game we didn't think we should have done but there you go, that's football, you have to look at the positives.
"If you're a penalty taker and you miss, you get asked questions but if you put it in the bottom corner no one says anything.
"If our performance levels stay like that we will be fine but you need to find the formula to win games.
"Marvin Emnes hit the crossbar when he only needed to side foot it from inside the six-yard box and it is those fine margins which are the difference between winning and losing football matches."
The home side started well as Clive Platt's header was saved by Jason Steele after five minutes, then Gary McSheffrey tested the goalkeeper with a left-foot shot from 20 yards.
Lita was the first Boro player to threaten, missing a header from Joe Bennett's cross in the eighth minute.
A scrappy period of play followed with neither side able to gain the upper hand – James McPake marshalling the Coventry box consistently, frustrating the visitors.
City's Lee Carsley miscontrolled a Richard Keogh cross and smashed over from inside the box, before Marlon King and McSheffrey brought saves out of Steele from free-kicks. The home side continued to dominate and Boro could only muster a weak header from Scott McDonald which failed to test Westwood.
However, Boro's confidence grew as they outpassed their hosts and Julio Arca curled a wicked 25th-minute shot in from the left wing which Westwood had to tip around the post at full stretch on 25 minutes. Tony McMahon could have scored from the corner but his header went wide.
Boro were given a great chance to take the lead when Lita was fouled by Nathan Cameron in the box but the striker's blast down the middle was blocked in spectacular fashion by Westwood.
Coventry started the second half with purpose and McSheffrey was unlucky not to hit the target with a drilled shot from the right.
Arca continued to threaten for Boro with crosses and shots from the left, before Lita went close again 10 minutes after the restart when his header from Marvin Emnes' cross went wide.
Discipline was poor throughout with the fouls creating a stop-start rhythm which benefited neither side .
Michael Doyle shot over the bar from distance in the 74th minute as the hosts wrested back some control of the match – and their hard work paid off when Matthew Bates fouled McSheffrey. King took his chance from the spot.
Mowbray replaced Arca with Kris Boyd as he sought an equaliser, with McSheffrey making way for defender Jordan Spence.
The visitors pumped crosses into the Coventry box but to no avail as Boothroyd's team held firm.
Coventry City: Westwood, Keogh, McPake, Cameron, Wood, Gunnarsson (Eastwood 68), Carsley, Doyle, McSheffrey (Clarke 83), King (Jutkiewicz 82), Platt. Unused substitutes: Ireland, Bell, Cranie, Baker.
Middlesbrough: Steele, McMahon (Hoyte 79), Wheater, Bates, Bennett, Emnes, O'Neil, Bailey, Arca (Boyd 80), McDonald, Lita. Unused substitutes: Coyne, Kink, Hines, Tavares.
Referee: D Whitestone
Man of the match: Keiron Westwood.