JOIN USForward Guillermo Rojas put the CONCACAF champions ahead in the fifth minute and midfielder Sergio Busquets equalised for Barcelona after 35.
Ballon d'Or winner Messi came off the bench to wild cheers from the near-capacity 40,952 crowd at the Zayed Sports City in the 53rd minute and put the European champions ahead almost immediately.
Barcelona increased their lead when a fine run down the left and into the box by Andres Iniesta ended with Pedro scoring from close in.
Barca meet Argentina's Estudiantes, the South American champions, in the final on Saturday.
Atlante went ahead after five minutes when their Argentine keeper Federico Vilar punted a free kick deep into the Barcelona half, defender Rafael Marquez missed the ball and Rojas darted through, lobbing keeper Victor Valdes and turning it into the net.
Busquets equalised 10 minutes before halftime with a low right-footed, first-time shot. Messi, having been a doubt for the match with a right ankle injury, came on for midfielder Toure and within two minutes had put Barca ahead.