For the first 60 minutes Zenit were comfortably two goals ahead through a fist half header from Pogrebnyak then a wonderful solo effort from Portuguese star Danny on 58 minutes.
At this stage United had been second best for most of the game as Zenit had looked the sharper and more determined to win what has been described as a European version of the Community Shield.
Reds boss Sir Alex Ferguson had been insistent this was a cup he wanted to win and only after the Russians were two goals clear did his team make any attempt to get a result.
Suddenly it was United who looked the stronger side and their dominance was rewarded on 72 minutes when defender Nemenja Vidic forced the ball home from close range.
The United chief acknowledged his side only came to life once they were behind.
He told ITV1,"We probably played our best football when we were two goals down and then we created one or two chances, but it was a very warm night, an open game and their were some tired players out there at the end.
"Tevez was outstanding, he was fantastic. We had some of the best chances in the match, but that happens.
Ferguson also felt that Zenit could be a force in the Champions League this season.
"They are a very good team, they'll do well. They have good movement, they are strong, yes I think they have a good chance.
Initially the United boss was philosophical about Scholes dismissal saying it was, "an instinctive thing he did, a bit unfortunate." But when it was pointed out Scholes would miss a Champions League game Ferguson looked shocked and mumbled, "is that right, it happens."