Trialist Romeo Castelen, a right winger formerly of Feyenoord and Hamburg, fired Blues into a fifth minute lead and the visitors had a string of opportunities to extend their lead further.
However Leon Lobjoit pulled the Sky Blues level in the 68th minute before Adam Barton completed the Coventry comeback five minutes from the end.
It left development squad manager Richard Beale to reflect on what might have been for his side.
"I'm disappointed," Beale told bcfc.com. "I've just had the boys in the changing rooms and told them that unless they can be consistent and maintain a performance for 90 minutes then they are not going to get anywhere.
"We were excellent first-half and created a number of chances but failed to convert them. No problem, come in at half-time at 1-0, keep a clean sheet in the second-half and the game would be won but they couldn't do that.
"They just switched off and perhaps the lads thought the job was done. They sat back allowing Coventry to come on to us and you're always going to invite pressure and as a result we conceded two goals.
"We created chances but failed to take them. It's those little details that make the difference with the transition from reserve football to the first-team."
For the third consecutive Professional Development League 2 North fixture, Beale named Papa Bouba Diop as one of his three eligible overage players. Pablo Ibanez and former Netherlands international Castelen filled the other overage berths while first-team goalkeeper David Lucas took his place between the sticks.
Callum Reilly was again deployed as an advanced midfielder behind lone frontman Marcel Henry-Francis.
And Blues got off to the perfect start. Henry-Francis linking up with Castelen for the 29-year-old to weave his way into the Coventry box and finish smartly.
It looked as though another would be around the corner for Blues. Diop flashed a low 25-yard drive just wide of the mark while Henry-Francis also tried his luck from distance with a half-chance.
Former Senegal star Diop should have been celebrating his third goal in as many games in the 38th minute when he met Castelen's cross only to direct his powerful header well wide.
Coventry 'keeper Lee Burge was almost left red-faced shortly before the break when his weak clearance fell to Mitch Hancox 40 yards out but he managed to nervously scamper back to get a hold of the Brummie's audacious effort.
Hancox was a livewire for Blues throughout and ended the first-half with a thumping shot, from a half cleared corner, that was well kept out by Burge.
At the other end moments earlier, Lobjoit had been guilty of directing a free-header from Chris Hussey's free-kick from the right horribly wide of Lucas' goal.
That miss looked to have been Coventry's only chance of getting back into the game as Blues started the second-half strongly.
Hancox's excellent cross from the left fell perfectly for Ryan Higgins but he could only direct his shot straight at Burge. Moments later, left midfielder Hancox burst into the box and saw a thunderous shot palmed away by Burge at his near post.
With Blues still only holding on to slender lead, Coventry were prepared to give up and when Hussey rattled the upright from a free-kick, the Sky Blues sensed a comeback. And when Lobjoit neatly directed a low shot from 18 yards beyond the reach of Lucas, Coventry smelt blood.
However even at that stage of the game, Blues still had chances to secure a second successive win. Only Aaron Phillips' last-gasp block denied Henry-Francis from 15 yards while Blues substitute Jack Deaman sent a free-kick hurtling towards the top right-corner only to see Burge's gloves get in the way.
The Sky Blues took the lead in the 85th minute as Hussey squared back for Barton to fire home from eight yards.
The hosts still had to be alert to further threats as Diop's low free-kick crept through to Burge while substitute Josh Hawker headed a Higgins corner over.
Coventry City U21s: Lee Burge, Aaron Phillips (C), Chris Hussey, Billy Daniels, Joe Henderson, Reece Brown (Ryan Haynes 80), Will Roberts, Leon Lobjoit, Shaun Jeffers (Ben Maund 90), Adam Barton, Courtney Baker-Richardson (Lewis Rankin 77).
Subs not used:Jack Finch, Ivor Lawton.
Scorers: Lobjoit (68) and Barton (85)
Blues U21s: David Lucas; Ryan Higgins, Will Packwood (C), Pablo Ibanez (Emmit Delfouneso 67), Ben Gordon; Romeo Castelen (Jack Deaman 67), Eddy Gnahore (Josh Hawker 67), Papa Bouba Diop, Mitch Hancox; Callum Reilly; Marcel Henry-Francis.
Subs not used: Callum Preston, Brice Ntambwe.
Scorers: Castelen (5)