Elliott Ward thrashed the spot-kick home to earn the Sky Blues a point and keep Barnsley in deep relegation trouble.
"I thought we did enough in the game to win and take the three points," said Davey.
"We had some great chances and got our goal early and when we needed to defend we defended. It's cruel.
"I don't know if it was a penalty but all I've got is a referee six yards away giving a corner and a player in the dressing room with a red mark on his chest."
Davey also questioned the Football League's decision to put such an inexperienced referee in charge of the game.
He added: "When you look at it in hindsight, the importance of the fixture, you would expect a more experienced referee in.
"They need someone with an old and experienced head that makes the right decisions 95 per cent of the time, not 60 per cent. It's not an apprenticeship."
Barnsley would have moved four points clear of the drop zone had they have held on for the win, but Davey will not allow his players to let the late equaliser affect their focus.
He said: "We have got to make sure the result and the lateness of the penalty does not affect us. We know what we have to do to make sure our status is right.
"We have got a point, it's another point someone else has to get."
Coventry boss Chris Coleman admitted he had sympathy for long-time friend Davey after the late action.
"It's harsh for Simon, we have all been there. It will be a tough one for him to swallow I imagine," Coleman said.
"He is good enough to keep Barnsley up in the league and he is big enough to take any criticism."
Despite the backing for Davey, Coleman was in no doubt that the penalty was the right decision.
"When it happened I thought it was a penalty, then I wasn't so sure. But I have seen it in slow motion and there is no doubt whatsoever, he had his arm out."
Coventry were lively during the first half and hit the bar, but they struggled to make an impact after the break and the home fans showed their frustration on several occasions, but Coleman defended his players.
"If there was booing there was booing," he added. "There was no lack of effort tonight. We kept going and kept going and we got a point.
"If the boys work like that for the last two games, I won't give them any problems."