The Argentina international started Wednesday's second-leg at Camp Nou from the bench after he picked up a knock in the 2-2 first-leg draw, yet was forced to come on around the hour mark with Barca trailing 1-0.
The Catalans then went on to equalise inspired by Messi and eventually progressed to the next round on the away-goals rule.
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"We knew that having him on the pitch would be important. He's our reference. He can pass, he can score goals; he can do everything. He helps us a lot."
Pique then went on to stress that the Blaugrana fully deserved to qualify for the semi-finals of the European elite this season.
"This club has shown a lot of quality in the last few years. We deserve to be in the semi-finals again," he added.
"In the first leg they scored in the last minute; we deserved a little more. We are happy to qualify for the semi-finals."
The draw for the final four takes place in Nyon on Friday.