However, with Nemanja Vidic and Rio Ferdinand the regular centre-back pairing of choice for Alex Ferguson, Pique only featured in 12 Premier League games prior to re-joining Barca in 2008.
And it was a game in Pique's final season - a 1-0 loss to Bolton when the 20-year-old was hauled off after 59 minutes - which Rooney believed spelled the end for his time at Old Trafford.
"Bolton away more or less finished Gerard Pique's career at United," Rooney wrote in his column for The Sunday Times.
"He was young and got bullied there and I think that's when Fergie decided that, physically, he wasn't right for the Premier League.
"I always remember Vidic: if we were going to Bolton — and it was the same when he was about to face Didier Drogba — he would be in the gym for two or three days before, pumping himself up."
Bolton's only goal that day came courtesy of Nicolas Anelka, when he took advantage of a mistimed Pique leap to score.
Pique has since gone on to win 28 major honors with his boyhood club Barca.
The defender also has over 100 caps for Spain and was part of La Roja teams that won World Cup 2010 and Euro 2012.