Inter had won their last seven Serie A games as they launched an unlikely title challenge under Claudio Ranieri following their miserable start to the season.
But Guillermo Giacomazzi scored for Lecce five minutes before half-time and Inter, despite having two goals disallowed, could not find a response, leaving them nine points behind leaders Juventus, who beat Udinese on Saturday.
It was Inter's second disappointment of the week after they were knocked out of the Coppa Italia by Napoli on Wednesday.
But they had plenty of chances to take the lead in the first half, Diego Milito firing wide from inside the box after 10 minutes, before Wesley Sneijder brought a good save out of Massimiliano Benassi with a strike from distance moments later.
At the other end, Luis Muriel twice tried his luck, first giving Julio Cesar a simple save, then firing wide, before Juan Guillermo Cuadrado went narrowly wide from outside the box.
On the half-hour, Sneijder put in a good cross for Walter Samuel, whose header was well saved by Benassi, and the keeper then denied Giampaolo Pazzini following good work from Esteban Cambiasso.
Benassi was again in the action after 34 minutes to save Samuel's goalbound header.
But it was Lecce who took the lead, Giacomazzi pouncing to fire home a right-foot shot from close range from Massimo Oddo's cross.
The withdrawal of the injury-prone Sneijder at half-time may have worried the Inter fans, though he was not displaying any obvious discomfort.
And without him Inter twice had the ball in the net. First Cambiasso pounced after Ricardo Alvarez's corner was flicked on by Samuel, then Milito tapped in in similar circumstances, but both times the offside flag was up.
And if Inter had not already realised it was not their day, a string of saves from Benassi confirmed it.
First he kept out Alvarez's shot from outside the box, then he saved from Maicon after Mauro Zarate had done brilliantly to beat three Lecce defenders.
But he saved the best for last, producing a miracle stop to repel Pazzini's close-range header from an Alvarez free-kick a minute from the end.