The Germans' 7-0 aggregate victory was Barca's worst-ever European defeat, and although Vilanova recognised that the World Player of the Year's recurring hamstring injury had played its part in the Catalans' dismantling, he denied that their dependence on him has grown substantially this season.
"He played in Bilbao on Saturday (when Barca drew 2-2) because he felt better. He imprinted a change on the team but at the end of the game he felt some strange sensations," Vilanova told a press conference.
"He trained yesterday and today, but he didn't feel right. He is an explosive player and there was a risk he could tear (his hamstring), so he couldn't help the team in these conditions.
"All these years when we have played without Leo we have won games by small margins, but this year in the league we have won games 5-0 and 3-0 without him on the pitch.
"When you have a player that is so good, it is normal that you notice it. If Bayern had been without (Franck) Ribery or (Arjen) Robben they would not be at this level."
Vilanova also rejected the claim that a clear-out is needed at the Camp Nou in the close season, but admitted that Bayern's physical superiority had played a crucial role in both legs of the tie.
"All squads are reinforced every season. I said the other day that we didn't need to change much, but rather recuperate the players we do have," he said.
"Bayern have arrived at this point with all their players and we have many out. Despite the great squad that we have you cannot win all the titles either. You can't win everything and the first leg has weighed heavily on this game."
Midfielder Xavi Hernandez echoed his manager's view that injuries and physical inferiority had played their part, but admitted that Bayern had also been tactically and technically superior.
"The team has tried, a 4-0 was practically impossible and with Robben's goal it was impossible," he told Canal Plus.
"Bayern were better. They dominated all the facets of football, tactically they are very good, physically very strong and mentally they were superior.
"The absences of (Carles) Puyol, (Eric) Abidal and today of (Sergio) Busquets and Messi is not an excuse, but they weakened the team."