The Argentine striker was not fully fit after a hamstring injury when he came off the bench to help Barca past Paris St Germain in the quarter-final on Wednesday (April 10).
The World Player of the Year played the final half an hour at the Nou Camp but was clearly not fully fit and he will probably be rested when Barca travel to Real Zaragoza on Sunday (April 14) in the league.
Barcelona, 13 points clear of their arch rivals and defending champions Real Madrid at the top, are closing in on a fourth title in five years and can take a step closer to dethroning the champions with a win.
Coach Tito Vilanova is likely to field a considerably weakened team at Zaragoza to keep key performers fresh and avoid any more injuries ahead of the Champions League semi-final, first leg in two weeks' time.
Barca assistant coach Jordi Roura said the club would be closely monitoring Messi's recovery.
"Luckily his injury has not got worse. He will follow his process and we will see how he is doing. We hope he is completely fit and that he can be with us," said Roura, referring to the Bayern semi-final first leg in Munich on April 23. The second leg in Spain is on May 1.
Roura said the semi-final was going to be between the two best European teams over the last few years.
"In the past years we have probably been the two best teams in Europe. We won't be surprised by Bayern. They beat Arsenal and Juve in the last 16 and the last eight in a very solid way. They are very strong, they are going to be a very tough rival. We all know it is going to be a very complicated and hard semi-final."
Roura was pleased Barca had avoided a 'clasico' with Real Madrid in the semi-finals. Real will take on Dortmund on April 24 with the second leg on April 30.
"There is no doubt that everything is magnified when there is a clasico," added Roura.
"A semi-final is always very interesting but there might not be as big a media coverage as if we were playing against Real Madrid. So, we are probably calmer. But I think the tension level in the semi-finals will be very high."