Both sides were in the hunt for third place in Serie A but Fiorentina had the fresher ideas and moved a point above their hosts and to within three of AC Milan, although they had much to thank goalkeeper Emiliano Viviano for.
The on-loan Palermo keeper made a string of saves in the second half to preserve Vincenzo Montella's side's lead in Rome.
Jovetic wasted a good chance to give the Viola the lead in the eighth minute when he blazed his shot over the crossbar from close range.
The visitors looked keen to take advantage of Lazio's tiredness after a Europa League trip to Stuttgart on Thursday and Juan Cuadrado was next to try his luck, hitting the target in the 14th minute, but not beating Federico Marchetti.
Jovetic did manage to beat Marchetti in the 19th minute, though, his precise shot from the edge of the area finding its way just inside the post.
It took Lazio a while to come to terms with conceding but they improved as the first half wore on, with Andre Dias missing their best chance in the 38th minute.
But Fiorentina struck again early in the second half with Ljajic curling in a direct free-kick with Marchetti somewhat to blame for failing to monitor the side of his goal not covered by the wall.
The response from Lazio was instant this time with Hernanes' free-kick soon tipped over the crossbar by Viviano.
Minutes later, Sergio Floccari's shot was diffused by Viviano, who was then not tested again until the 85th minute when he denied Libor Kozak.
It was too late for Lazio to salvage anything from the game at that stage and Floccari's shot, which met Viviano's legs, summed up a miserable night for the Rome club, who slipped below Fiorentina in the standings.