James Meredith's first goal in just under a year looked to have set City on their way to a home win but Rovers substitute Charlie Colkett's equaliser four minutes before the end of normal time snatched a share of the spoils for the visitors.
The goal was all the more frustrating for City to take as it appeared Romain Vincelot was all set to clear the danger before the ball fell to Colkett, but the Frenchman unfortunately slipped over.
Despite Colkett's late intervention, City still nearly managed to secure the victory in the final minute of an eight-minute injury time period but Haris Vuckic's close range header was somehow clawed off the line by Rovers 'keeper Kelle Roos.
The extended over-time period was due in part to a second half stoppage of over three minutes after two low-flying drones were spotted above the Northern Commercials Stadium.
Speaking after the game, McCall said: "There is naturally some frustration around - a home draw is never what we would ideally be looking for.
"I felt the first half was even, we knew Bristol Rovers would be competitive, but in the second period we moved the ball a lot better.
"The tempo of our play, the atmosphere generated from the crowd, it was all there for 30-35 minutes.
"The way we played for the most part was really enjoyable to watch but I guess you can't legislate for a slip from Romain. It wasn't an error from him it was just disappointing how it has happened.
"For them to score so late on after dominating the second half was definitely sore to take.
"I was really pleased with the way we played after the break, we just couldn't get that second goal to finish things off.
"I thought it was in (from Haris Vuckic's late chance) but somehow their 'keeper has dived back to save it on the line.
"I think it would have been a result we deserved if the ball had of gone in but it wasn't to be.
"There were still plenty of positives to take out of this game though, especially in the second half.
"We moved the ball quicker, created a lot more chances and got into better areas on the pitch.
"The lads were distraught in the dressing rooms afterwards because it is frustrating to take when you have controlled a half for so long as we did in the second half and not gone on to win."
This Saturday's result, coupled with defeats for Northampton Town and Bolton Wanderers, means that McCall's men are now the only unbeaten side left in Sky Bet League One this season.
McCall added: "There are no easy games in this division.
"If you look at the results today (Saturday), there have been a number of sides near the bottom beating sides near to the top.
"We knew Bristol Rovers would be another tough one for us - they have a great work ethic - but the way we took the game to them in the second half really pleased me.
"We take the positives, move on and look forward to next Saturday's game at Bolton."