Barca's title was confirmed with victory at Deportivo La Coruna.
Messi, who hit a hat-trick, said: "It's a shame, like when Xavi or [Javier] Mascherano left, symbolic players for the club.
"This year it was up to Andres. [It is] a pity for us and for the club.
"He leaves in the best way, although we regret that it wasn't with the Champions League and a treble.
"It is a double that he more than deserves. I am very happy for him and we wish him the best."