Ronnie Moore claimed Tranmere had outplayed Stevenage, despite Greg Tansey's equaliser meaning the game ended all-square at 1-1.
Jake Cassidy, on loan from Wolves, looked to have earned all three points for Rovers when he headed home with 12 minutes to go in Saturday's League One clash at Broadhall Way.
But Cassidy's 11th goal of the season was not enough to see off Stevenage as Tansey fired home from the edge of the area in the 92nd minute.
The draw actually extended Tranmere lead at the top of the table to three points and Moore refused to be downbeat.
"I don't think you can do much about the goal to be honest. I don't think he knew where it was going and it's ended up in the back of our net," said Moore.
"But we've been fantastic. I've got nothing but praise for our lads, they were brilliant. When you consider Stevenage are a big, strong side, we've not given them a kick.
"We've footballed them to death, we just haven't been ruthless enough in and around the area, that's the only thing that was missing for me. I'm not going to rant and rave. We're gutted because it's happened once or twice too often.
"Our goal was a fantastic move, but I thought we did that nearly all day. I just felt that the final ball in the box wasn't quite there. That's the only criticism I have. I'm just gutted that we're not going away with the three points, it would have been a fantastic win because I thought we were streets ahead of them."