The Argentine forward netted with a stunning strike in Barca's 2-1 semi-final first-leg win at the Estadio Vicente Calderon last Wednesday but he was also booked late in that match for a foul on Filipe Luis.
Another yellow in Tuesday's return fixture at Camp Nou would mean a suspension for the 29-year-old and if Barca - as is expected - were to advance to the final on May 27, the five-time Ballon d'Or winner would be unable to take part.
Along with Messi, defenders Jordi Alba and Samuel Umtiti are also just one booking away from a ban but Barca boss Luis Enrique claimed that it would not affect his plans for Tuesday's match.
"It won't change anything," he told reporters, "because fortunately these players are very good at knowing the situation. I don't think it is going to affect how these players play in the game. The most important thing is to beat Atletico Madrid and get into the final."
Sergio Busquets and Andres Iniesta are available again after injury and could feature against Atleti but Neymar is suspended and misses the meeting with Diego Simeone's side.