The Montenegro striker embarrassed defender Lucio by nodding in Daniele De Rossi's cross to give struggling Roma a first league win in their fifth game of the season and inflict Inter's first Serie A defeat.
The goal came completely out of the blue in the game between last season's champions Inter and runners-up Roma, with Rafael Benitez's visitors having the better chances before being caught cold in the fevered atmosphere of a rocking Olimpico.
Dejan Stankovic rattled the bar from distance for Inter in the first half and stand-in Roma goalkeeper Bogdan Lobont saved well from Samuel Eto'o in the second.
Indebted and up-for-sale Roma denied former Italy boss Marcello Lippi had been lined up to replace Claudio Ranieri in midweek and the side fought hard for their coach in a game which started promisingly but became niggly with four players on each side booked.
The hosts were better organised than in recent insipid displays with De Rossi, Francesco Totti and John Arne Riise back from injury and will now by buoyed for Tuesday's Champions League game with CFR Cluj.
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Treble winners Inter, who host Werder Bremen on Wednesday, still lead the table with 10 points as they seek a sixth straight scudetto but can be overhauled by a number of clubs after Sunday's main programme of matches.
Like Roma, Milan have not looked title material so far and needed Zlatan Ibrahimovic to score again in a 1-0 home win over Genoa which moved the Rossoneri up to fourth.
Milan, third last term and without a scudetto since 2004, recorded only their second league win thanks to the Swede netting his second goal in Serie A and fourth overall since he joined on loan from Barcelona.
The former Inter frontman prodded home four minutes into the second half following Andrea Pirlo's assist.
Genoa had dominated the first period, forcing Milan keeper Christian Abbiati into one spectacular save at a nervous San Siro.
"I'm tired but it needed real sacrifice to win," said Ibrahimovic who pressed the opposition more than fellow forwards Ronaldinho and Robinho.
"Nothing depends on just one player," the Swede told reporters. "We are 11 on the pitch. If we do our work we will come out on top."
Milan have failed to fully gel under new coach Massimiliano Allegri but the narrow win after two successive league draws will give the side confidence for Tuesday's Champions League match at Ajax Amsterdam.
The weekend matches went ahead after a Serie A players' strike was postponed following constructive talks between the union and the league in a dispute over a collective contract.
