The Seasiders ended their own run of five games without a win to record only their second win in 11 games and revive their own play-off hopes.
DJ Campbell made the point save for the home side deep into five minutes of stoppage time with his first goal since returning on loan for Ian Holloway's side.
However the home fans had to endure a nervous second half which saw the dismissal of central defender Rob Edwards on the hour mark and a penalty miss by Boro with just seven minutes remaining.
This after Brett Ormerod had fired Pool ahead on 30 minutes with his seventh goal of the season, but after dominating proceedings Pool were put on the back foot once Edwards had been dismissed for bringing down Barry Robson when clean through.
Gordon Strachan's men then squandered a golden chance to level things on 83 minutes, however the home fans' despair turned to delight with a superb full-stretch save by Matt Gilks from Scott McDonald's spot-kick.
Middlesbrough's visiting fans can't help, but have been disappointed by the manner their side meekly surrendered their unbeaten run and a season's double to the Seasiders on a poor surface.
Blackpool dominated throughout with home keeper Gilks being forced into one notable save other than the penalty, keeping out a week shot by Boro's out-of-sorts forward Jeremie Aliadiere.
Ormerod hit the sidenetting midway through the first half before Campbell blazed over from ten yards just minutes later.
However, the home side were soon ahead when Ormerod fired home from a tight angle, after being fed by a clever back-heel from Gary Taylor-Fletcher.
Ormerod was denied by the legs of Boro keeper Danny Coyne just before the break, but after the restart it looked as though Pool had shot themselves in the foot when Edwards stumbled after receiving an awkward pass and bundled Robson to the ground.
But Blackpool in the end held on comfortably and fully deserved their win.