Inter went close early on having recycled possession, which allowed Yuto Nagatomo to unleash a 25-yard strike that was well held by Fiorentina keeper Norberto Neto.
La Viola hit back when Giuseppe Rossi and Joaquin combined well as the Spaniard used his pace to break clear, smashing his shot at goal, but Samir Handanovic saved well to put the ball behind for a corner. Minutes later Fiorentina wasted another good chance as Borja Valero flashed wide from range.
Fiorentina should have gone ahead in the 27th minute when Valero found Joaquin in the box, but he drilled just inches beyond the far post.
Fiorentina broke the deadlock in the 59th minute as the in-form Rossi stepped up to crash home a penalty, after Joaquin was fouled in the box.
However, Inter took their chance to hit back in the 73rd minute when Esteban Cambiasso made the most of a goalmouth scramble to bring the scores level.
The game looked to be heading for a draw in the closing stages, but Jonathan made the most of a poor first touch to crash home a fierce strike and give his side a home victory.