Striker Akwasi Asante had marked his return to action with the opening goal for the hosts after just four minutes.
However the Sky Blues fought back to level just before the break through Will Roberts before Billy Daniels fired home a smartly-taken winner in the 70th minute.
Development squad manager Richard Beale used up all of his overage berths by naming Darren Ambrose, Morgaro Gomis and Hayden Mullins in his starting XI. Colin Doyle also took his place, as well as the captain's armband, between the sticks.
Blues couldn't have got off to a better start thanks to Asante's poacher instincts. The 20-year-old capatilised on a misplaced pass at the back for Coventry and found the net with a low shot from the edge of the area.
At that point, Blues looked to go on to extend their lead further. Apart from Doyle being called on to keep out Shaun Jeffers' stooping header, the hosts had the better of the chances.
Ryan Higgins tried his luck from distance before failing to make the most of an Ambrose shot that had rebounded off the post. Amari'i Bell then picked out the head of Mullins with a corner from the right only for Chris Dunn to make a good save.
However Coventry were level in the 37th minute when Danny Phillskirk's cross from the left found Roberts inside the Blues area and he diverted his effort beyond Doyle.
Blues still continued to make chances. Asante was denied by a good save from Dunn at his near left post while Koby Arthur sent a powerfully-struck shot fizzing inches wide of the other stick.
Lee Carsley's Coventry stepped it up a gear after the break and, after Callum Bell's 20 yard effort had been tipped away by Doyle in the 66th minute, they took the lead four minutes later.
Daniels picking his spot with a low shot from 25 yards that beat the outstretched arm of Doyle and nestled into the bottom corner.
Ambrose could have equalised for Blues in the 89th minute but sent Arthur's squared ball over from six yards.
Blues U21s: Colin Doyle; Ryan Higgins, James Fry (Eddy Gnahore 87), Emmitt Delfouneso, Amari'i Bell; Koby Arthur, Morgaro Gomis, Hayden Mullins, Darren Ambrose; Reece Hales, Akwasi Asante (Jack Deaman 60).
Subs not used: Nick Townsend, Charlee Adams, Liam Truslove.
Coventry City U21s: Chris Dunn, Jordan Clarke, Ryan Haynes, Josh Ruffles, Joe Henderson, Jordan Willis, Will Roberts, Billy Daniels, Callum Ball (Ben Maund 87), Danny Phillskirk, Shaun Jeffers.
Subs not used: Ivor Lawton, Louis Garner, Lewis Rankin, Jack Finch