With Barca trailing, the Argentine entered the fray on 60 minutes and managed to hit two goals in the last seven minutes for an improbably victory.
Messi insisted afterwards: "The pass from Xavi was good for me to play it over the goalkeeper. The match had been greatly complicated by the first-half, but in the second we dominated more. We deserved to win.
"With this result, we're virtually through to the next round.
"The coach is the one who decides rotations, but I'm ready to play every game and when appropriate. I feel happy for the goals that I scored and by the triumph."