A Phil Jones own goal was cancelled out by Dimitar Berbatov’s strike, and United went into the lead through Darren Fletcher on the hour mark before being pegged back by Pablo Aimar.
The result moves the Portuguese team to top of Group C on the basis of the two teams’ results against each other, and Jorge Jesus’ side face hapless Otelul Galati at home in their last game.
The English champions meanwhile must travel to Switzerland to take on Basel, who are only a point behind United currently.
Despite the Old Trafford team being put into an uncomfortable position, the Scottish coach has full belief in his players.
“It’s going to be a hard game but the chips are down for us and I’ve got every confidence in my team,” he told Sky Sports.
“That was very disappointing. We played so well tonight. We made a lot of good chances, played some really great football. I have no fault with my players at all. They deserve better.
“That’s the game. It’s a cruel game at times and it was cruel for us tonight.
“(It was) a bit freakish to be honest with you – an own goal and then a bad kick out from David De Gea.
“I think we had to get into a rhythm and a tempo. We had a bad start. It was a goal after three or four minutes. It does take the steam out of you, it takes the wind from your sails a little bit.
“Once they went to the game they played really well and they should have maybe been two or three up at half-time. I think it was very unfortunate we didn’t win that game,” he concluded.
United are back to domestic duties at the weekend, and host Newcastle at home on Saturday.
By Gareth McKnight