In a contest that was low on entertainment, Felipe Caicedo netted the winner with a 42nd-minute penalty as he punished a mistake by goalkeeper Ivan Provedel.
When Provedel misjudged a touch inside his box, Caicedo nipped in and was brought down by the 24-year-old. The Ecuadorian forward then struck the resulting spot-kick past him in confident manner.
Simone Inzaghi's Lazio move up three spots into the Champions League places, two points above AC Milan and three above Atalanta and Roma.
Roma are at Chievo on Friday night and then Atalanta and Milan host SPAL and Cagliari respectively on Sunday.
Guiseppe Iachini's Empoli, with their winless streak having extended to eight league games, remain one place above the relegation zone, a point better off than 18th-placed Bologna, who are at home against Genoa on Sunday.