Atalanta goalkeeper Andrea Consigli blocked Milito's weak spot kick in the 23rd minute. He then also stopped a dangerous header from Walter Samuel on the ensuing corner, and Inter didn't come close again.
It was the fifth consecutive league match Inter failed to win at the San Siro, despite a changing-room speech from club president Massimo Moratti at halftime. On Tuesday, Inter was eliminated from Europe by Marseille after allowing late goals in both legs, raising questions about whether manager Claudio Ranieri will last until the end of the season.
"We didn't need this, but this is the way the entire year has gone," Ranieri said. "Now we've got to do well in the upcoming matches and work professionally, but without giving the fans any illusory goals like third place."
Third-place Lazio struggled in a 1-0 loss at Catania, which won with a volley from former Juventus defender Nicola Legrottaglie in the 80th.
AC Milan leads with 60 points, Juventus is next with 56 and Lazio has 48. Napoli and Udinese have 47 points each and Roma, Inter and Catania are tied for sixth with 41 each.
Milan beat Parma 2-0 Saturday and Juventus routed 10-man Fiorentina 5-0.
In the night match, Napoli fought back for a 2-2 away draw against 10-man Udinese.
Giampiero Pinzi and Antonio Di Natale had scored for Udinese before Diego Fabbrini picked up his second yellow card in the 60th. Udinese defender Maurizio Domizzi then handled the ball in the ball in the 73rd. Edinson Cavani missed the ensuing penalty, but then made up for it with goals in the 81st and 85th.
Roma hosts Genoa on Monday.
Elsewhere, Lecce and Palermo played to a 1-1 draw in a match that both sides ended with 10 men; Bologna and Chievo Verona drew 2-2; and Novara beat Siena 2-0 for its second consecutive win since rehiring Attilio Tesser as manager.
Earlier in the lunchtime fixture, Chilean striker Mauricio Pinilla scored a hat trick as Cagliari beat nine-man Cesena 3-0 to end a three-match losing streak in its first match since Massimo Ficcadenti returned as manager.
Pinilla scored from close range in the 14th minute and then added penalties in the 45th and 56th to give him seven goals since transferring from Palermo in January.
Cesena midfielder Giuseppe Colucci picked up his second yellow card in the 60th and defender Marco Rossi also got his second yellow, in the 79th.
Ficcadenti was rehired last weekend to replace Davide Ballardini.