A 1-1 draw on Wednesday night at the Camp Nou saw the Spaniards progress on away goals with the sides level at 3-3 on aggregate after two legs.
Messi, who started on the bench due to a recent hamstring injury, came on with Barca trailing but helped them get the goal that they needed to go through.
"He was the catalyst; we changed after he came on and we have to thank him for that," Pedro is quoted as saying by BBC Sport.
"It doesn't matter to us who we get in the semi-finals as all of the teams in the draw will be very difficult to play against."
The draw for the semi-finals of the Champions League will be made on Friday.