Messi completed the 90 minutes in the 3-1 win over Napoli at Camp Nou on Saturday night as Barca advanced to the final phase of the competition.
However, the Argentine attacker took a heavy knock to his ankle as he was fouled by Kalidou Koulibaly and won a penalty late in the first half.
The Barca captain missed training on Sunday, but was present at the club's Sant Joan Despi training base on Monday to continue his recovery and preparations for Friday's game, even though coach Quique Setien had given the squad a day off.
All of Barcelona's players will return to training on Tuesday, before travelling to Lisbon on Thursday ahead of the one-off game against Bayern the following day.
Messi's spectacular goal against Napoli on Saturday means he has now scored against 35 different teams in the Champions League, which is two more than Juventus' Cristiano Ronaldo.
Setien said on Saturday that the six-time Ballon d'Or winner had taken a "heavy knock" against Napoli, but was confident the 33-year-old will be fine for Friday's game in Lisbon.