The game was fizzling out into a 1-1 draw at the Riverside after a George Friend opener for Boro had been cancelled out by Yossi Benayoun just before the break.
But Rangers were gifted a goal out of the blue as home goalkeeper Dimi Konstantopoulos went to clear a back-pass and a deceptive bounce followed by his air shot left Bobby Zamora free to tap in.
The London outfit sealed victory soon after through Ravel Morrison
"I don't believe it," Karanka said. "I can explain what happened but I can't understand it. It has happened again.
"It was a game we did not deserve to lose. We had a good chance to win at one end and then suddenly we have lost the game.
"There was not much between the teams and we had chances but every week it is the same story. I just wish one game it would be us scoring in the last minute."
But Karanka refused to blame keeper Konstantopoulos for the pivotal moment.
"I don't blame him," he said. "We are a team. We win as a team and we lose as a team. Yes, he has made a mistake - the ball looked to bounce - but it doesn't matter who makes the mistake.
"For the rest of the game he played well and for 85 per cent, 90 per cent of the game the team played well and for this I am happy."
- Sports & Recreation