Forward 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.
"When he (Messi) goes on to the pitch the dimension changes completely -- he comes from a different galaxy," Atlante coach Jose Guadalupe Cruz told a news conference.
"You have to recognise that he's brilliant but also the team coordination helps a lot."
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.
Vilar dived to his right to save a header by Busquets from a corner from the right taken by Xavi in the seventh minute.
The Mexican side could have had a second three minutes later when right back Navarro sprung the offside trap to run through on goal, but instead of shooting he elected to pass, failing to find his two team mates in the middle.
BARCA EQUALISER
Busquets equalised 10 minutes before halftime with a low right-footed, first-time shot from the left after Yaya Toure had flicked on with his head a corner from the right by Xavi.
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.
He made a diagonal run into the box from right to left, racing on to a fine through pass from Zlatan Ibrahimovic, and rounded Vilar who managed to get a touch to Messi's shot but could not prevent it from going in.
"It's not the first time Messi gets on to the pitch and scores. He's very competitive and he always decides the final score, he goes on to the pitch and he is a fighter," said Barcelona coach Pep Guardiola.
"His physical state is good and his mind is in a perfect frame to go out and win."
Pedro added the third goal in the 67th minute when he hit the ball past Vilar after Iniesta had won it on the left and made a jinking run into the box.
The 22-year-old forward now has a remarkable record of having scored in all six competitions Barca have taken part in this year.
Atlante striker Rafael Marquez broke away on the right with a good chance to reduce the deficit but his shot was saved one-handed by the advancing Valdes.
Substitute Bojan Krkic fluffed an excellent chance right in front of goal to increase Barca's lead and they could have scored again from several late moves with Messi causing havoc in the Atlante defen
