The Spanish champions won the Champions League for the third time in six seasons, and beat United for the second time in three, as Van der Sar's glittering career ended in defeat and three goals in the back of his net.
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"We made one or two mistakes, and they punish you," he said.
"It was one game too many for us I think. It's not nice to lose of course but they had the better chances.
"I don't know if I could have prevented (Lionel) Messi's goal. I thought I was positioned well but I think (David) Villa was blocking my sight. Messi tends to curl it to the far post and he just clipped it around Villa.
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"They are very good. We started well in the first 15 minutes, same as we did (against Barca in the 2009 final in) in Rome, and you just have to try and score the first goal but we didn't do that."
Barcelona took the lead when Pedro scored after 27 minutes with a wide open part of the goal to aim at Van der Sar's left, and went back in front after Wayne Rooney's equaliser when Messi scored after 54 minutes with a shot that curled away from him, again to his left.
Although he kept Barca at bay with one or two important saves, he was powerless to stop David Villa making it 3-1 after 69 minutes with a lofted curling shot, but kept the score down with more saves before the end.
'FANTASTIC CAREER'
Despite the disappointment, Van der Sar has had a great career with the Netherlands, Ajax Amsterdam, Juventus and Fulham, moving to Manchester United in 2005 and playing a key part in United's success since then including winning the Premier League title earlier this month.
"It's not always given that your career ends on a good note but I thank everybody for the memories and we'll see each other again," he said.
United manager Sir Alex Ferguson, still seeking to finalise the Dutchman's replacement next season, said: "Edwin has been a fantastic servant to Manchester United, we wish him well.
"He's had a fantastic career and he's had that great career with tremendous honour and I think that's the thing that stands out about him."
Van der Sar was not the only one of United's old guard to have a disappointing night as Ryan Giggs, 37, the only survivor from their 1999 Champions League winning team, was peripheral to much of the action.
Although he helped set up Rooney's goal, he lacked his usual spark and passing accuracy and for the first time in many matches, gave a lacklustre performance.
Paul Scholes, 36, who could yet retire befor
