The Catalan giants were troubled by the Scottish champions for the second match in a row after they produced a last-gasp winner to deny the Hoops at the Nou Camp a fortnight ago.
Last night on Glasgow soil, Neil Lennon's men took it right up to the Blaugrana and eventually produced a dream result thanks to goals from Victor Wanyama and Tony Watt before Lionel Messi grabbed a late consolation.
Vilanova said he was aware it would be a difficult fixture for his star-studded line-up, although they had a makeshift defence, but he was complimentary of the way that Celtic played in front of their fanatical fans at Parkhead.
"First of all I would like to congratulate Celtic, the fans were amazing tonight," said Vilanova.
"Before we played I knew they were good at set-pieces and we didn't want to concede too many and we didn't give them too many chances.
"But I can't be satisfied because we want to win the game.
"It is a really difficult stadium but we were like the home team and we locked them in the box.
"But you are never happy when you don't win.
"If we had scored first it might have been a different game.
"But they scored first which allowed them to defend and their goalkeeper (Fraser Forster) was brilliant tonight.
"It is not the first time we have lost a game like this and it won't be the last."