Diego Milito took a pass from Inter captain Javier Zanetti and scored his 22nd goal of the season to break the deadlock in the 57th minute at Siena's Artemio Franchi stadium.
Inter finished with 82 points, two more than AS Roma, which won 2-0 at Chievo Verona.
Roma scored both of its goals in the first half and had its hands on the title before Milito saved Inter.
Inter beat Roma in the Italian Cup final, and Jose Mourinho's side will face Bayern Munich in the Champions League final Saturday as it attempts to become the first Italian club to achieve the treble.
Also Sunday, Sampdoria beat Napoli 1-0 to clinch fourth place and the final Champions League berth.
Giampaolo Pazzini scored with a header in the 51st minute for Samp, redirecting a free kick from Reto Ziegler for his 19th goal of the season, and Sampdoria goalkeeper Marco Storari made two good saves from shots by Fabio Quagliarella to preserve the lead.
Afterward, Sampdoria celebrated to the tune of the Champions League music.
Palermo came into Sunday with a chance of finishing fourth but needed a slip-up from Sampdoria, rendering its 2-1 win over Atalanta meaningless.
Edinson Cavani scored twice for Palermo, including the winner from a penalty five minutes into added time.
Otherwise, all of the key places in Serie A had already been decided.
AC Milan, which beat Juventus 3-0 Saturday, finished third while Napoli and Juventus had already clinched sixth and seventh to round out the Europa League places.
Atalanta, Siena and Livorno were already relegated to Serie B.
In other games, it was: Bari 2, Fiorentina 0; Cagliari 1, Bologna 1; Catania 1, Genoa 0; and Parma 4, Livorno 1.
The most anticipated games naturally involved Inter and Roma.
While its hopes relied on Inter failing to win, Roma took the initiative with first-half goals from Mirko Vucinic and Daniele De Rossi.
Vucinic put Roma ahead with a long-range shot in the 39th minute and De Rossi doubled the lead with a shot from 25 meters (yards) in the 45th. Roma captain Francesco Totti had already hit the outside of the post in the 22nd.
In Siena, the host had a chance when Albin Ekdal sent an effort wide in the sixth minute but Inter dominated otherwise. It had a tough time finding the target, however.
Inter's 18-year-old forward Mario Balotelli was wide from a sharp angle in the 13th and Milito slid the ball past Siena goalkeeper Gianluca Curci a minute later but it rolled just wide of the empty net.
Curci made a reflex save from a header from Milito in the 22nd, then saved a header from Inter defender Walter Samuel in the 30th.
In the 38th, Balotelli hit the crossbar with a spectacular bicycle kick and Samuel headed high in the 44th.
Inter midfielder Esteban Cambiasso was then wide with a shot from the edge of the area in the 55th.
Even after Milito's goal, Inter had trouble sealing the victory — and a draw would have given the title to Roma.
A shot from Dejan Stankovic skimmed off the top of Siena's crossbar in the 75th.
In the 88th, Inter goalkeeper Julio Cesar had some trouble gathering the ball directly in front of his goal, but eventually got control as defender Marco Materazzi stood guard and Inter then waited anxiously before celebrating at the final whistle.
