Portsmouth scored the only goal seven minutes into stoppage time to give their Championship survival hopes a huge boost and inflict major damage on Middlesbrough's fast-fading automatic promotion bid.
The visitors didn't have a shot on target until Andre Dozzell's volley deflected in off Conor Chaplin in the final seconds, bringing to an end an eight-game winless run for John Mousinho's side.
Boro are now winless in six and three points behind second-placed Ipswich, who have two games in hand, after Kieran McKenna's side won at Norwich at lunchtime.
Portsmouth looked set to fall into the relegation zone until Chaplin's winner, which keeps Mousinho's side a point and a place above the bottom three.
Boro had 20 shots compared to Portsmouth's three but the Teessiders have now scored just four goals in their last six games, two of which came in Monday's draw at Swansea.
Kim Hellberg's side started well and Alan Browne forced a good early save from Nicolas Schmid after being teed up by Jeremy Sarmiento. From the resulting corner, centre-back Adilson Malanda had a shot deflected onto the roof of the net.
For all Boro dominated the ball in the opening 45 minutes, they struggled to create meaningful openings and that Browne effort was the home side's only effort on target until Dael Fry's close-range header was saved by Schmid in the last minute of the first half.
Boro could have opened the scoring two minutes into the second half when David Strelec split the Portsmouth defence with a through-ball but Schmid denied Riley McGree with his feet.
Boro then had a glorious chance to break the deadlock when Tommy Conway robbed Regan Poole of possession midway inside the Portsmouth half, sparking a two-on-one home attack.
Rather than shoot, Conway opted to try and tee up strike partner Strelec but his pass was intercepted by Madiodio Dia, the only covering defender, and Poole then recovered to block the rebound from McGree.
Conway again chose to pass rather than shoot when he had another opportunity soon after and this time his attempted through ball for McGree bounced off defender Jordan Williams and rolled agonisingly wide of Schmid's left post.
Portsmouth launched a rare attack at the midway stage of the second half and Terry Devlin picked out Colby Bishop but the striker's audacious flick went wide.
Boro very nearly forced a breakthrough in added time but half-time substitute Sontje Hansen saw his shot cleared off the line by Dozzell.
Portsmouth then won a corner at the other end and Fry's headed clearance only reached Dozzell, whose first time strike deflected in off his team-mate.
Middlesbrough's Kim Hellberg:
"I'm disappointed, devastated. The performance was poor, actually. First half was terrible. It was like watching paint dry. I don't know why, I must have failed with everything I told them before the game because we weren't good enough.
"Second half, we come out better. Our best spell was in that first 15-20 minutes in the second half when we created enough to at least score the goal. But we are not efficient enough to do that.
"Again, we created most of the chances, but this performance was not good enough.
"It was boring, it was lazy, there was no energy, except in that first 15-20 minutes in the second half.
"In the first half, it's slow, it's boring, it's no energy. It's passive. That is the disappointment.
"But, I want to be clear, we should not lose this game. This was poor by the high bar we've set ourselves. We maybe don't deserve to win, but you cannot lose this game when they have no chances in the whole game."
Portsmouth's John Mousinho:
"It's an amazing result at this stage of the season. It's all about picking up points and we managed to do that.
"If you're asking me about the result in isolation, we've come here to hopefully win the game and we've managed to do that in those circumstances, which was different to what we've been doing in recent weeks. It's a brilliant three points for us.
"This Middlesbrough side are such a good team, they've been in the top two for 90% of the season.
"They have brilliant attacking players, brilliant defensive players as well. They're so dangerous and that was part of the reason we set up as we did.
"We had to defend for long stages and get through some dark moments for the boys at the back.
"We did get lucky, let's be honest we got lucky, but that's something we just haven't had this season. It tends to be the case when you're down the bottom."
