The Granata climbed to sixth in the table with a fifth win from eight games thanks to Cerci, who won and converted a penalty on the hour mark at the Stadio Olimpico.
Mid-table Atalanta offered little by way of response until the final stages and would live to regret not snatching a late equaliser given Immobile squandered the chance to double Torino's advantage at the death.
Davide Brivio was sent off for up-ending Matteo Darmian in the area, but Immobile fired straight into Andrea Consigli's gloves from the spot.
Torino were denied the rub of the green in the opening minutes as Cerci saw his fourth-minute strike ruled out for offside and, in the 12th minute, Gerard Vives saw his tricky shot punched clear by Consigli.
The hosts looked the better side for most of the first half, and Darmian was unlucky to see Gugliemo Stendardo head his goalbound free-kick off the line shortly before the half hour.
Cerci looked for Nikola Maksimovic from a corner, but the Serbian could not direct his back-post header on target.
The last solid chance of the half fell to Torino, but again Consigli got the better of the Granata attack by parrying Cerci's dangerous cross to safety.
Giampiero Ventura's men went back on the attack when play resumed, Immobile heading Darmian's deflected shot over the bar in the 53rd minute.
They were handed a clear opportunity to finally take the lead on the hour mark as Consigli was adjudged to have fouled Cerci in the Bologna box.
The Italy winger composed himself before coolly steering the ball home to register his 10th goal of the season.
Atalanta suddenly decided to wake up and Stendardo came within inches of levelling the match, but his header from a corner veered just wide of the mark.
Then, Torino keeper Daniele Padelli, who enjoyed a very quiet afternoon, was alert to push German Denis' close-range header on to the angle of post and bar.
Consigli was the last keeper to the face a real test of skill, though, after Brivio felled Darmian to hand Torino a late penalty.
The Atalanta defender saw red, but Immobile could not capitalise as Consigli guessed right to keep the spot-kick out.