Boro were left reeling after Andre Ayew's late penalty saw Swansea to victory at the Liberty Stadium.
Neil Warnock watched his side dominate proceedings - they had what looked like a certain goal disallowed - yet his men looked like being left to count the cost of conceding a messy goal themselves until Sam Morsy struck in the dying moments.
But Swansea hit back later still through a controversial penalty, scored by Andre Ayew, to take victory.
Had Marc Bola’s 46th minute effort not been disallowed, you would have backed Boro to go on and claim all three points, but in the end Neil Warnock's side return home empty-handed.
Boro had gone into the game on the back of a midweek win at Coventry, coming from behind to win 2-1, and Warnock had made three changes for the clash with Swansea. Match-winner George Saville was joined by Duncan Watmore and Yannick Bolasie in returning to the starting line-up.
Boro had the first sight of goal when Anfernee Dijksteel had a shot deflected wide after a quick break by Saville. That proved to be the last action for Dijksteel, who was forced to leave the field injured after being clearly caught off the ball by Ryan Manning earlier in the contest before being caught late again.
Swansea had to be on their toes when Bola got in behind and looked to tee up Duncan Watmore, but the ball was forced out for a corner. Home goalkeeper Freddie Woodman was called upon for the first time properly when Bolasie tried his luck from distance, but it was routine for the keeper.
What threat the home side posed had been dealt with efficiently by Boro, Marcus Bettinelli was a complete spectator, until moments before half-time. The visitors' defence failed to deal with a header into the box and the ball fell kindly to Andre Ayew who had a deflection to thank for his shot creeping inside the near post.
It was an ill-deserved goal, and left Boro having to come from behind in a game once again.
Chuba Akpom was introduced in place of Watmore at half-time, and Boro had the ball in the back of the net within a minute of the restart. Bola smashed the ball home after some good attacking play, but referee Gavin Ward was quick to blow up, citing a foul by Yannick Bolasie during the build-up. The reaction of the Boro players was one of bafflement at the decision - on review, the Boro man took a kick in the build-up, not the other way around.
Warnock’s side were showing spirit and Swansea were forced into a real rearguard action as Boro laid siege to the home side’s penalty area. Saville sent a header wide, Dael Fry had one deflected for a corner, and the Swans threw themselves in the way of everything.
It looked as though some justice had been done when Sam Morsy's shot found a way past Freddie Woodman and into the net.
But there was more frustration to come for Boro, when the referee awarded the Swans a last-gasp penalty, having initially appeared to signal a corner following a challenge from George Saville.
Ayew stepped up to convert the penalty and compound Boro's misery.