Marvin Emnes clawed back a leveller three minutes into second-half stoppage time to earn a point after Chris Basham stabbed home from a free-kick seven minutes from full-time.
Before that Boro had enjoyed the bulk of the possession and caused Blackpool plenty of problems while attacking down both flanks.
"It was a bit frustrating," Mowbray said. "Getting a point was the least we deserved and yet it was a game we all felt we should have won.
"Yes, the equaliser came at the death and it has taken the sting out of what would have been a very disappointing defeat but we feel we should have taken all three points.
"It would have been an injustice if we hadn't got something. We got our just reward in the end.
"I couldn't see them scoring to be honest. Defensively we looked solid and we didn't look like we would concede and then we were undone by a momentary lapse at a set-play.
"That said, we didn't make our possession count. We have said it before but we have to be more productive with our opportunities."
Blackpool boss Paul Ince was dismayed his side had let their 100 per cent start to the Sky Bet Championship season slide away following wins over Doncaster and Barnsley, but he was prepared to see the positives.
"It was two points lost for us definitely," he said. "When you are a goal up at 90 minutes you expect to hold on.
"I was surprised they got it back at that point but, then again, it happened for us at Barnsley last week when we snatched it late on so you always know it is possible.
"I thought we got it tactically spot on for most of the game. We stopped them playing and I thought they were running out of ideas so to lose it then was disappointing.
"But you can't argue with the lads. They give you everything. They have cuts and bruises and everything. The team spirit has been fantastic.
"We should be sat here now with nine points but if you had said to me that three games in we'd have the seven points I'd have taken that.
"It's a fantastic return really, especially given our problems with injuries and a depleted squad."