Danilo D'Ambrosio and Ashley Young scored in the opening 20 minutes as Inter finished the season with 82 points, one behind leaders Juventus who lost their final game 3-1 at home to AS Roma.
Atalanta, whose last defeat was at home to SPAL in Serie A in January, finished third with 78 points. The hosts appeared to have one eye on their Champions League quarter-final against Paris St Germain on Aug. 12.
Barcelona weighing up move for Manchester City midfielder Silva - Paper Round
Inter Milan were off the mark in less than two minutes when Atalanta goalkeeper Pierluigi Gollini flapped at a corner and D'Ambrosio headed into the net. Gollini was injured in the process and had to be replaced by Marco Sportiello.
Ashley Young extended Inter's lead with a delightful goal after 20 minutes, cutting inside and then curling the ball past Sportiello from the edge of the area.
Last month, Conte, frustrated after seeing his team let several games slip from their grasp, said he was not interested in the race for second place.
"I say it's the first of the losers. There are those who are content with this, but it has no meaning for me," he said.
Barcelona and Manchester City plot surprise summer swap deal - Euro Papers
Expert view: Is Fonseca the right pick for Spurs?
Spurs 'call off pursuit' for Conte as new manager - reports