The centre-back was dismissed in the second half for two bookable offences and Vilanova revealed that he had warned the Spain international at the interval.
"At half time, I told Pique to be careful as his next foul would most likely result in a second caution," Vilanova told reporters after the game.
"Even if his sending-off was for a clear foul, there must have been 200 other cases similar to his tonight. I don't have to add more."
The defeat ended a 19-game unbeaten run for Barca.