The defender's own goal was sandwiched between strikes from Arjen Robben and Thomas Muller, as the Bavarians ran out 7-0 aggregate winners and set up an all-German final with Borussia Dortmund.
Messi played no part in the game, remaining an unused substitute following a recurrence of an old injury, but Pique believes the Argentine could have done little to turn the tie around.
"Messi is the best in the world. Obviously it's not the same without him on the pitch but I don't think things would have been so much different with him," he explained after the final whistle.
"It's not pleasant living a situation like this one. We tried in the first half but after the first goal we just fell apart. The last 45 minutes were so hard."
Barca president Sandro Rosell, meanwhile, highlighted Messi's absence from the second leg, while admitting that Bayern was superior.
"If the best player in the world is not on the pitch, the team is not the same but all players play hard and believed and we showed that Barcelona know how to win and how to lose. It's the coach who decides with the staff and the doctors. They take the decision and we just accept it," the chief explained.
"We have to congratulate Bayern. They were clearly the better team and deserve to be at the final in Wembley."
Xavi was another Blaugrana representative with high praise for the Germans, who he believed were worthy winners against his club.
The midfielder told Canal Plus: "We had many problems in defense with [Carles] Puyol, [Eric] Abidal, [Javier] Mascherano, [Sergio] Busquets and [Lionel] Messi too... but we can't look for excuses, Bayern were better.
"It's not fair saying German football is better than Spanish only because of these matches. Our team is still a good team and one that can keep on winning for many years, even if we didn't know how to play against Bayern or Real Madrid."