Claudio Ranieri's side were unable to find a way through against the visitors as they recorded their fifth home league game in a row without a win, and Atalanta had a valid penalty shout of their own turned down towards the end of the game as neither side found a breakthrough at the Giuseppe Meazza stadium.
Inter were missing the creativity of Wesley Sneijder in midfield and the Dutchman's incisive eye could have made the difference, especially in the first half as Inter enjoyed the better of the possession but with little cutting edge.
The home side did manufacture an opportunity in the 22nd minute when Giampaolo Pazzini won a penalty, tangling with Gianpaolo Bellini as both went down. The referee deemed the Atalanta captain to be the guilty party when it appeared that it was a fairly even-handed wrestling match, but nevertheless Bellini was booked and the spot-kick given.
Atalanta goalkeeper Andrea Consigli was more than up to the task however when Milito stepped up, getting down to his left to save. From the resulting corner Consigli denied Walter Samuel from point-blank range with a smart stop, in what were the busiest two minutes of the opening 45.
Joel Obi flashed a fierce volley just over from 20 yards and Consigli was again called into action when he blocked a low Pazzini shot, as the sides went in goalless at half time with Inter pondering their missed opportunity.
The second half saw Atalanta lose Guido Marilungo to injury and Consigli was again alert when he palmed away a stinging shot from Andrea Poli. Julio Cesar was given his first real test when Atalanta substitute Manolo Gabbiadini glanced a header towards the top-right corner, but the Brazilian athletically pawed the ball away as the stalemate rumbled on.
Atalanta had what looked to be a certain penalty denied with just over 10 minutes remaining when Gabbiadini, who was impressive throughout his second-half cameo, was brought down by Lucio. The Inter defender's clear trip on his opponent was not viewed as being sufficient grounds for a spot-kick for the visitors, as they continued to search for an opening.
In additional time Ezequiel Schelotto almost found Gabbiadini with a ball flashed across the face of Inter's goal, but there was to be no winner as the game ended goalless after five minutes of added time.
The result leaves Inter in seventh position in the Serie A table, with Atalanta in 12th spot.