Having fallen to a surprising home defeat against Serie A newcomers Como on Tuesday, Atalanta looked desperate to prove a point in the early stages, with Ademola Lookman seeing a low effort smartly saved by Lukasz Skorupski.
The hosts grew into the contest as the first half progressed, but clear-cut chances came at a premium as both defences held firm under pressure.
La Dea remained the more threatening of the two sides in the final third and Skorupski again came to Bologna’s rescue, thwarting a close-range strike from Marco Brescianini.
Gian Piero Gasperini’s men continued to probe for a breakthrough before half-time, but substitute Samardzic dinked a half-chance over the bar as the scores remained level at the break.
After a disjointed first-half display, the hosts made a dream start to the second period, with Santiago Castro turning superbly on the edge of the box and curling a clinical strike into the far corner to open the scoring within a minute of the restart.
However, any momentum generated from that goal was soon extinguished when a sloppy piece of defending from Jhon Lucumi resulted in the Colombian bringing down Charles De Ketelaere and receiving a red card.
Armed with the numerical advantage, Atalanta came within inches of finding a swift leveller when Raoul Bellanova powered an effort against the bar from inside the box.
Desperate to avoid a fourth defeat in six Serie A matches this season, La Dea continued to dominate possession in pursuit of an equaliser, and after several missed chances, it finally arrived in the final minute of regulation time.
Picking up the ball on the edge of the box, Samardzic created a yard of space for himself before unleashing an unstoppable strike into the corner beyond Skorupski, denying the Rossoblù a first home Serie A win since April.
Flashscore Man of the Match: Santiago Castro (Bologna)
