The result edged Atalanta closer to the Champions League qualifying places with eight games remaining, while Bologna dropped back into the relegation zone only four days after climbing out of it.
Josip Ilicic put Atalanta ahead with a delightful curling effort in the third minute and the Slovenian added a second from a tight angle two minutes later.
He then set up Hans Hateboer for the third after nine minutes before Duvan Zapata burst down the left to score the fourth on the quarter hour mark with his 20th league goal of the season.
It was the first time a team had scored four goals in the opening quarter of an hour of a Serie A match since 1932.
Bologna, missing forward Mattia Destro after he was injured celebrating the winning goal against Sassuolo on Sunday, pulled one back with a Riccardo Orsolini free kick nine minutes into the second half.
Atalanta are fifth with 51 points, one behind AC Milan, while Bologna are 18th with 27 points after being overhauled by Empoli who beat Napoli 2-1 on Wednesday.
Sassuolo ended an eight-match winless run as they hammered hapless bottom club Chievo 4-0 in Thursday's other match, helped by two first-half goals from Merih Demiral and one apiece from Manuel Locatelli and Domenico Berardi after the break.
(Writing by Brian Homewood; Editing by Christian Radnedge)
