The La Liga leaders were thumped 4-0 at the Allianz Arena last week, with the Argentine playing despite only recently recovering from injury.
However, Vilanova is certain that Messi can make the difference in the return leg.
"We know how important Messi is in this team," Vilanova said. "And even more in front of goal.
"The better he feels, the more chances we have to go through. This would have to be done between us all, but yes, if Leo is okay, he will have something to say."
The two sides meet in the second leg at the Camp Nou on Wednesday night.