The Argentine struck in the 23rd minute with a fine finish to a breakaway move to cancel out Robinho's stylish ninth minute opener, which came during a frantic opening period of pressure from the home side.
Barcelona moved up to seven points, with unbeaten Milan in second spot on five, two ahead of Celtic who beat Ajax 2-1 in Glasgow.
Milan came racing out of the blocks, putting pressure on Barca's backline and a defensive error led to Robinho's goal.
The Brazilian beat the away side's dithering defenders to a high ball, and after exchanging passes with countryman Kaka, slid a simple finish past Victor Valdes.
The home side rarely looked troubled in the opening period, but found themselves back to square one 14 minutes later after giving the ball away sloppily to Andres Iniesta.
"The lads played an excellent match, we gave little away but still created a few good chances. Pity about the (Barca) goal, we were punished for a mistake," Milan coach Massimiliano Allegri told reporters.
The Spain midfielder slipped in Messi on the right, who after cutting inside drilled low to level the scores just as he looked to have lost his footing.
Barca dominated the second half against a tired Milan, but despite a couple of good chances couldn't make the most of their possession and had to settle for a point.
"We lost two points... because we created more goal chances and for this reason we deserved a victory," said Barcelona's coach Gerardo Martino.
"It's not easy to play with so many players spread across your opponents' midfield."
(Editing by Rex Gowar)
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