Marvin Ekpiteta’s fine touch and turn led to the Tangerines defender cancelling out Marcus Tavernier’s eighth-minute opener just after the hour.
And Middlesbrough defender Grant Hall was left with his head in his hands after he turned a corner into his own net in the 78th minute to hand Blackpool a second win since returning to the second tier of English football.
Ekpiteta and Tavernier’s goals drew complaints from the opposition and in the end it was Hall’s own goal that proved decisive in giving Neil Critchley’s side all three points.
Boro boss Neil Warnock was annoyed with referee David Webb for awarding the visitors a free-kick that led to the equaliser, as well as how his side ended up losing.
He felt Onel Hernandez had been fouled but it went the other way with Webb seeing an infringement by Tavernier.
Warnock, whose side have dropped to 16th and lost Anfernee Dijksteel with a hamstring problem, said: “It wasn’t a foul, simple as that. The referee was pretty consistent in not giving fouls but that was not a foul in a million years.
“Having said that, you still have to defend the goal. I think the free-kick is played and nobody runs across to it, I think it was Isaiah Jones. The cross then comes in and Dael gets turned, I am disappointed to concede like that.
“I am disappointed we haven’t won the game. That’s life. Things happen. We could have been out of sight by half-time, the injury to Dijksteel, not having a full-back on the bench, cost us. I thought we were comfortable before that.
“I thought it was a good game. I thought we are a little short on numbers. We can’t get it going consistently, we don’t have that ruthless streak at times.
“I can’t fault them effort-wise, or for their technical ability, but it’s about finding that little bit extra. Until we get clean sheets we won’t get where we want to be. To lose a game from a corner kick is comical really.”
Blackpool boss Neil Critchley said: “We can take great heart from winning at Middlesbrough.”
Middlesbrough: Lumley, Dijksteel (Jones 56), Hall, Fry, Peltier, Howson (Ikpeazu 88), Lea Siliki (Payero 79), Tavernier, Crooks, Hernandez, Sporar. Unused substitutes: Olusanya, Watmore, Bamba, Daniels.
Blackpool: Maxwell, Sterling, Ekpiteta, Keogh, Garbutt, Bowler (Lawrence-Gabriel 90), Wintle, Dougall, Anderson, Lavery (Yates 86), John-Jules (Madine 71). Unused substitutes: Connolly, Husband, Carey, Grimshaw.
Referee: D Webb (County Durham).