Edoardo Reja's men will have to settle for a place in Europa League next season after missing out on qualification for the continent's elite tournament
Diego Milito opened the scoring in the first half from the penalty spot, but the Biancocelesti staged a complete comeback with Libor Kozak, Antonio Candreva and Stefano Mauri netting after the break to help Edoardo Reja's men to the three points.
In the end, however, the result was rendered insignificant as both teams missed on qualification for next season's Champions League as Udinese defeated Catana to secure third spot in Serie A.
The game got off to a slow start as both sides employed a cautios approach in the early minutes of the match. Senad Lulic went close for the Biancocelesti in the 11th minute when he sent a shot from outside the box just wide of the right post.
Lazio continue to press and nearly got ahead through Candreva, whose scorching effort narrowly missed the target. Inter managed to get themselves together and created a chance of their own before the half-hour mark when Fredy Guarin had a shot from outside the box saved.
The Colombian had another chance shortly after, but once again was denied by Albano Bizzarri in goal for Lazio. Milito wasted a double chance before he was trusted with the responsibility to take a penalty for a foul on Maicon by Cristian Ledesma in the 45th minute.
The Argentine was merciless, skillfully converting from the spot to give the Nerazzurri the lead just before half-time.
Lazio looked rejuvenated after the break, and threw everything forward in search of a comeback against Andrea Stramaccioni's men.
In the 57th minute Ledesma tried to make amends for conceding the penalty, but saw his shot from outside the box saved by Luca Castellazzi. Candreva was next to test the goalkeeper, but he too was denied by the 36-year-old.
Moments before the half-hour mark, Kozak drew the game level by heading in a cross from Ledesma as the Nerazzurri were caught napping by the Biancocelesti. Andrea Stramaccioni's men, however, did not suspect what was in store for them as in the 63rd minute they conceded another goal.
Lulic went on a marvellous run down the left flank, before finding Candreva near the penalty spot. The Juventus man controlled the ball before slotting in with a powerful finish on the volley, which left Castellazzi helpless.
Inter tried to come back into the game in the remaining minutes of the match, but could only hit the post through substitute Giampaolo Pazzini.
Lazio punished the Nerazzurri's reckless charge in the closing moments of the game through Mauri, but It hardly mattered in the end, as Udinese 2-0 win over Catania meant both clubs missed out on Champions League football.