The 44-year-old was left frustrated by the Spaniard's red card which sparked a stunning comeback that ended their unbeaten run in La Liga
Vilanova's side appeared to be cruising thanks to early goals from Lionel Messi and Pedro, but they ceded their 19-match unbeaten streak in the Primera Division and eventually lost 3-2.
"Even if his sending-off was for a clear foul, there must have been 200 other cases similar to his tonight," Vilanova told reporters after the match. "I don't have to add more.
"At half-time, I told Pique to be careful, as his next foul would most likely result in a second caution," he added.
But the Barca boss also praised Philippe Montanier's side, adding: "Credit to Real Sociedad.
"Their win is more due to their merit, rather than us not playing well. I have nothing to reproach the players for."
The Catalan giants have now failed to win at Anoeta in three consecutive seasons, and club captain Carles Puyol was quick to point out their opponent's strength at home.
"We should have scored more in the first half, but even if we had a 3-0 lead, it would not have been over, they have a great team," the veteran said.
Xavi echoed his compatriot's comments: "It's a pity, we could have gone up with Messi's shot against the post in the first half. The loss had to happen one day though, let's move on."
In spite of the loss, Barcelona still lie top of La Liga, 11 points ahead of second-placed Atletico Madrid.