Giacomo Bonaventura's strike midway through the second half was enough to earn Atalanta all three points and take them above AC Milan into mid-table in Serie A.
The 24-year-old earned Stefano Colantuono's men all three points after they survived a first-half storm which saw Cagliari hit the woodwork twice.
Victor Ibarbo was denied twice by the post and he let his frustration get the better of him late on to earn a red card and compound Cagliari's misery.
Ibarbo benefitted from the suspension of Nene to make his return to the Cagliari starting XI, and he soon showed what he is all about, flashing a shot with his left foot which struck the post in the seventh minute.
Not long after, Ibarbo hit the woodwork once again with another venomous left-footed effort.
Atalanta responded to the close shaves with German Denis sending in their first shot of the game in the 17th minute, only just missing the target.
Cagliari continued to threaten more, though, and Daniele Conti's free-kick struck the outside of the post as they went close once again.
The first moment of danger in the second half came at the other end of the field where Giacomo Bonaventura headed straight into the arms of Vlada Avramov.
Midway through the second half, Bonaventura took his second chance of the game to provide an acrobatic finish at the far post from Franco Brienza's cross.
Cagliari responded well and Conte went close to levelling and Andrea Cossu also only just missed out.
Atalanta's young goalkeeper Marco Sportiello then denied Francesco Pisano as Atalanta just managed to hold on, and incense Ibarbo, who earned a red card for retaliating late on.