The forward side-footed in a Daniele Mannini cross in the 72nd minute after a slip-up by Inter full back Davide Santon to give the Genoa side a home win and 15 points from six games.
Inter are in second spot two points further back and alongside Fiorentina after they won 1-0 at Livorno with a 76th-minute penalty by Stevan Jovetic.
Inter came close with a powerful Samuel Eto'o shot shortly before Pazzini struck but the champions could have few complaints about their first league defeat this term.
"It was a very important goal in front of this full house," Pazzini told Sky television. "We're top. It's a great night."
"We picked ourselves up immediately after Florence," he added, referring to Wednesday's 2-0 defeat at Fiorentina that ended a run of four wins.
The spot-kick was awarded for a foul by Marcus Diniz on Italy forward Alberto Gilardino, who will be suspended for Fiorentina's big Champions League clash against Liverpool on Tuesday.
