After the match, which Inter won 3-1, the Spaniard claimed that TV replays clearly showed that two of the Italian side's goals should have been disallowed, Diego Milito's for offside and Maicon's for a heavy challenge on Lionel Messi in the build up.
Barcelona were also denied what looked a clear penalty after Daniel Alves was brought down by Wesley Sneijder in the box. Benquerença overlooked the challenge and instead booked the Brazilian right back for diving.
"I have seen it on TV and you can see that Milito's goal was offside and Maicon's came after a foul on [Lionel] Messi," Pique said.
"We had no help from the referees. The second leg has to have an impartial referee.
"Inter knew us very well, they dominated the match and they knew how to stop our game."
Asked about the penalty decision, Alves said: "There was no was no way of playing the ball - I think it was a penalty because he caught my supporting leg."
Various Spanish media outlets have also reported that Xavi told Jose Mourinho the referee had been biased towards Inter because of his shared nationality with the former Chelsea coach.
The Barcelona midfielder is alleged to have asked Mourinho: "What did you think of the referee?" to which the 'Special One' replied: "Why are you asking me? What about the Chelsea match last season?"
When asked what had happened in the tunnel, Mourinho said: "It's always difficult to lose for those who aren't used to losing. I'm like that too. It's the characteristic of a team which always wins.
"I can never have a problem with Xavi because I adore him. He's one of best in the world."