The Argentine has been suffering from a hamstring injury since his heroics from the bench against Paris Saint-Germain earlier this month, which has resulted in the Spaniard acting as a 'false nine'.
However, the former Arsenal captain is adamant that he would be happy to be dropped from the side if it meant that he were replaced by Messi.
"Lionel is ready to play in Munich. He is the most important player of the team. We feel safer with him, as was shown against PSG," said Fabregas. "Leo offers us things no other player does. If I drop out because of Leo I would accept this because he is so important.
"I have played as a false nine four or five times but I feel more comfortable playing as an inside left. I know perfectly what my role in the team is. I feel more comfortable in my second season and I've had more continuity. It's been a big evolution for me.
"The level of demand is so high at the club. I have to give everything and in this club you have to accept criticism both at journalistic and street level. I cannot complain about how they treat me. I am happy with my number of goals and assists this season."
Barcelona face Bayern Munich at the Allianz Arena in the first leg of their Champions League semi-final on Tuesday night.