The Slovenian's 22nd-minute strike was a rare moment of quality in the first half, which was a largely dull affair.
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He beat Ivan Kelava with a brilliant 25-yard effort to register his second Serie A goal in Rossoneri colours.
Brazilian goalkeeper Gabriel - deputising for Christian Abbiati - had to make a fine stop to deny Antonio Di Natale in the 63rd minute, as he got a hand to the Italian's shot and pushed it onto the bar.
Milan saw out the victory, which takes them into seventh place with eight games played.