The Spanish team were crowned world club champions for the first time, denying Argentina's Estudiantes who took the honour in 1968.
In the 110th minute Brazil right back Daniel Alves crossed and Messi darted between two defenders to chest the ball past goalkeeper Damian Albil.
Estudiantes had shocked the large Barca support in the 43,000 crowd at Zayed Sports City when they went ahead in the 37th minute.
Hard-working captain Juan Sebastian Veron squared the ball to Juan Manuel Diaz and Mauro Boselli leapt between defenders Carles Puyol and Eric Abidal to head the Uruguayan's pinpoint cross past the diving Victor Valdes.
Pedro then nodded a dramatic equaliser in the 89th minute. A high cross came in from the left, centre back Gerard Pique touched it on and the substitute headed over Albil.
It was just reward for Barca's perseverance with their classy attacking game and snuffed out tired Estudiantes's dream.
"We played formidably, it was a victory we deserved. Six titles in a year is unequalled," coach Pep Guardiola told a news conference, referring to his team's Champions League, La Liga, King's Cup, Spanish Super Cup and European Super Cup wins.
"Pedro tried so many times to set up the (equalising) goal, finally he scored it."
In a first half with hardly any goalmouth action, Barca had more than 60 percent of possession but little penetration.
The European champions could have had a penalty when Albil came out for a through ball to Xavi and the midfielder went down.
MESSI CAUTION
Zlatan Ibrahimovic also backheeled to Xavi whose low cross went begging while Messi had a shot blocked.
Messi was later booked for diving as he could find little space in the packed Estudiantes defence.
Just before halftime he tried a quick flick into the box and Ibrahimovic attempted an overhead kick but failed to reach the ball.
With striker Pedro coming on for midfielder Seydou Keita and Messi attacking from deeper, Barca had more penetration after the break.
Messi found Ibrahimovic in space on the left but the Swede's shot went just wide of the far post.
Then, in the 52nd minute, Albil saved from Ibrahimovic who had forced his way through on the left.
Pedro almost converted a cross from Thierry Henry on the hour but failed to make contact with the goal at his mercy.
Barca should have scored in the 69th when Pedro had a shot blocked by Albil's feet.
The victory by Guardiola's team meant the trophy stayed in Europe after Manchester United beat LDU Quito 1-0 in Japan in 2008.
"What hurts most is we were so close with just minutes remaining but we were dignified in defeat. We lost to the best team in the world," said Estudiantes coach Alejandro Sabella.
"Estudiantes gave them a great battle, we were up to it (but) it wasn't enough. There's a thin line from happiness to tears."
