Referee Steven Cook awarded the spot-kick on the advice of a linesman after Rob Kozluk was adjudged to have handled Freddy Eastwood's volley, when the match official had initially awarded a goal-kick.
Defender Ward kept his cool to slam home his sixth goal of the season from the spot to leave Barnsley hovering just above the relegation zone.
Barnsley had looked set for victory when they went in front in the eighth minute when the speedy Jamal Campbell-Ryce delivered a left-wing cross to Daniel Bogdanovic.
The Malta international turned past Coventry defender Ben Turner to plant a ten-yard shot in the corner of the net.
The South Yorkshire team should have extended their lead when Jon Macken's cross from the right dropped perfectly to Bogdanovic, but this time he mis-hit his shot from close range.
Coventry had a great opportunity to level when Danny Fox's corner from the left was headed against the bar by Ward.
The second half started brightly and soon the Tykes' Hugo Colace forced a smart save from Kieren Westwood in the home goal.
However, the visitors then dropped the pace a little and seemed intent on keeping their vital lead intact, which they did with some ease.
Barnsley could and should have made sure of the victory in the closing stages, as goalscorer Bogdanovic shot over from 25 yards, before Macken passed up a chance to double the lead and seal the three points.
Those misses looked like not proving too costly, until the last-gasp drama which left Simon Davey's side facing an anxious end to the season.