AlexisSanchez leveled the score five minutes after Messi departed, toe-poking in a low shot after combining well with Cesc Fabregas for his 10th in La Liga.
The coach said both spot kicks were warranted, and came after a first leg in which Braca were denied a penalty despite AlexisSanchez being brought down.
He then set up AlexisSanchez two minutes later, and Barcelona looked set to win until Bilbao's Ander Herrera pounced on a loose ball to shoot just inside the post in the 90th.
Barca coach Josep Guardiola brought AlexisSanchez off the bench with just over 20 minutes to go, and the Chile forward made an instant impact as he bundled in an equalizer at the second attempt.