"The Argentine player has the green light from the doctors to take part in the crucial match against the German side," Barca said in a statement on their website.
Messi, who sustained the injury in the quarter-final first leg at Paris St Germain, had "completely recovered", the statement said.
The World Player of the Year missed Barca's last three La Liga games but came on for the final half an hour of the second leg against PSG to help the Catalans reach the last four on away goals.
Messi came off the bench to help rescue Barcelona's Champions League dream as a 1-1 draw with Paris Saint-Germain saw them into the last four on away goals in the quarter-finals.
Barca had appeared rudderless for large swathes of the match and seemed to be heading out of the tournament until the introduction of Messi changed the mood and destiny of tie that could have fallen either way.
Barca host Bayern for the return leg on May 1 and the successful side will meet Borussia Dortmund or Real Madrid in next month's final at Wembley.
BAYERN MUNICH: Neuer; Lahm, Boateng, Dante, Alaba; Martinez, Schweinsteiger; Robben, Müller, Ribery; Gomez
BARCELONA: Valdes, Alves, Bartra, Pique, Alba, Busquets, Iniesta, Xavi, Pedro, Messi, Sanchez.