Roberto Mancini's Inter missed out on Champions Leaguequalification when they lost 2-0 at Lazio last weekend but the win over Empoli means they are sure to play in the Europa League next season.
Ivan Perisic tapped home the winner before halftime after Manuel Pucciarelli's 37th-minute goal for the visitors had cancelled out an early opener from Mauro Icardi.
Icardi hobbled off later in the match with a thigh injury.
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"This remains Inter's best campaign in the last five years,"Mancini told Sky Sport Italia after his side took their points haul to 67 with one game to go.
"The position is all we deserve having thrown away all of our good work from the first six months."
Milan moved above Sassuolo into sixth spot on 57 points after Carlos Bacca's 40th-minute penalty downed Bologna who had Amadou Diawara sent off in the 12th minute.
While Milan can secure a European spot with victory over Juventus in the Italian Cup final on May 21, defeat would see the third Europa League berth awarded to the team finishing sixth in Serie A.
Sassuolo can climb back above Milan with a win at second-bottom Frosinone on Sunday.
(Writing by Ed Dove; Editing by Tony Jimenez)
