The Reds looked on course for a useful point and second clean-sheet in as many matches until home defender Dominic Hyam took advantage of a poor clearance to decide the contest in the third minute of stoppage-time.
Poya Asbaghi's valiant side, without a win on the road all season, battled hard in search of their fifth draw away from Oakwell but remain rooted to the foot of the table, nine points from safety.
Barnsley’s XI sported two changes from their 1-0 win over QPR in the form of Romal Palmer and Callum Brittain, who had been out since the Tykes’ 5-4 win over Barrow in the FA Cup in early January.
The Sky Blues made the early running and looked threatening down the left as top-scorer Viktor Gyokeres twisted and turned his way into the box before scuffing his effort into the hands of Brad Collins.
The Barnsley goalkeeper, who turned 25 on Friday, had to be alert again inside the first five minutes when Callum O’Hare’s sublime pass with the outside of his foot set Gyokeres free to force another save from him.
Waghorn was next to go close for Robins’ side when he met Gyokeres’ cross only to stab wide of the left-hand post.
Barnsley, who beat Coventry 1-0 back in August, weathered the storm and earned a half-chance themselves, but Michal Helik headed wide from a well-delivered corner.
O’Hare took aim at Collins’ goal again five minutes before the break and the former Chelsea academy man was up to the task as he beat away the midfielder’s effort before comfortably claiming Maatsen’s free-kick.
It was more of the same in the second half, with the Sky Blues looking for the all-important breakthrough.
Ben Sheaf’s clean strike was held by Collins as the brave Barnsley defence put their bodies on the line to block efforts from O’Hare and Jamie Allen.
It took until two minutes into stoppage time for Coventry to make their pressure pay as Sheaf’s hopeful ball into the box was not cleared by the Tykes defence and centre-back Hyam calmly turned and fired his effort into the bottom corner.
It was the second time in as many seasons that Hyam had netted against Barnsley, having popped up to help the Sky Blues to a 2-0 win over the same opposition at St Andrew’s back in April 2021.