Milito's weak spot-kick saved by Andrea Consigli after just 21 minutes of play and Inter never looked like scoring after that as their two-game winning streak in all competitions came to an abrupt end.
Lazio fell to a 1-0 defeat to Catania in Serie A.
The winner came with just 10 minutes to spare, as Nicola Legrottaglie rose highest to meet Francesco Lodi's corner and put the ball beyond the reach of Federico Marchetti.
In other matches, Alessandro Diamanti's 81st-minute equaliser handed Bologna a point in an exciting 2-2 draw against Chievo.
Marco Andreolli gave Chievo the lead after 26 minutes before Marco Di Vaio responded on the hour-mark for Bologna.
But parity lasted just 10 minutes as Cyril Thereau put Chievo in front again, only for Diamanti's late goal to ensure both sides would share the spoils.
Chilean Mauricio Pinilla scored a hat-trick - including two from the penalty spot - as Cagliari toppled a nine-man Cesena 3-0
Lecce and Palermo both finished with 10 men in a 1-1 stalemate.
Second-bottom club Novara won 2-0 at Siena.
Napoli surged late to nab a vital 2-2 draw with 10-man Udinese, as Edinson Cavani struck both goals for Walter Mazzarri's side.
Cavani missed a penalty with 15 minutes to play, but accounted for the mishap by firing home twice - firstly with a curling free-kick before tucking home a second from an acute angle - to salvage a point for Napoli.
Pablo Osvaldo scored an early goal as Roma saw off Genoa 1-0 in their Serie A clash at the Stadio Olimpico on Monday.
In a match dominated by the hosts, striker Osvaldo's goal in just the third minute proved the difference between the two sides.
Sixth-placed Roma have now moved to four points of Lazio, who occupy the third Champions League qualification spot.
