Boro took the lead in the 32nd minute when Ashley Fletcher scored for the third home game in a row, and they wasted a flurry of chances after that to see the victory through.
But for the second game inside five days, Middlesbrough allowed the lead to slip and ended up losing when Paul Gallagher’s 63rd minute free-kick was followed by Jayden Stockley’s header eight minutes from time.
Gallagher’s leveller had stemmed from the red card Daniel Ayala was issued for a strong, last-ditch challenge on Brandon Barker when referee Keith Stroud deemed it was out of control despite winning the ball.
Boro are now just three points clear of seventh and are 15 shy of second placed Leeds after winning just three of their last 14 games at the Riverside.
Pulis said: “Even before the red card, if you create the opportunities and chances we have, we’ve got to be more than 1-0 up. I have been at the club for 14 months and I haven’t stopped talking about the chances in the final third that we throw away.
“The first half performance was excellent and it warranted us being two or three goals up. Jonny Howson misses a chance, Aden Flint misses a chance. We have some great opportunities to score before they get the sending-off.
“The game should have been out of sight and that has been our Achilles heel since I’ve been at the football club. We dominated the game. Preston were very fortunate to be anywhere near us.
“The decision, I have watched it now on four different angles. The referee is a long way away from the challenge and he has players in between him. It looks for me that he can’t see the challenge because two of their players and one of our players is in the way.
“I have said to him that to make a decision like that you have to be 100 per cent sure, you can’t be 50 per cent or 60 per cent, otherwise you are gambling, and I think he gambled, he made a very, very poor choice and it affected the game.”