Ruslan Malinovskyi struck in the first half for La Dea, who were comfortably in control until Robin Gosens was dismissed for a second bookable offence midway through the second period.
The red card seemed to galvanise Roma and they drew level through ex-Atalanta player Bryan Cristante, as he fired in from the edge of the box. The Giallorossi also finished with 10 men however, as Roger Ibanez picked up two yellow cards in stoppage time.
An end-to-end start saw both teams have opportunities, as Edin Dzeko and Lorenzo Pellegrini went close for Roma, whilst Malinovskyi, Duvan Zapata and Josip Ilicic all fired at Pau Lopez from promising positions at the other end.
After a period of increasing pressure, Atalanta broke the deadlock midway through the first half. La Dea began a quick counterattack and Zapata spread it out left for Gosens, who in turn played the ball back into the box. Malinovskyi rushed in and squeezed between two defenders to prod the ball into the roof of the net.
Having taken the lead, Atalanta continued to press and Zapata stung Lopez’s fingertips, whilst the goalkeeper denied Remo Freuler with a good save after Roma gave the ball away in their own box.
Atalanta began the second half on the front foot and Gosens came close with a strike from the edge of the box, forcing Ibanez into an important block.
A rare Roma chance saw Jordan Veretout strike a freekick from a good position, but the Frenchman blazed over, whilst Henrikh Mkhitaryan weaved his way through and drilling a shot inches wide.
The best chance of the game fell to Atalanta substitute Luis Muriel however, as he was left in acres of space at the back post but somehow sliced wide from a low cross with the goal at his mercy.
Roma were offered a lifeline with 20 minutes remaining as Gosens was shown a second yellow card for a clumsy foul on Veretout, and Dzeko almost punished Atalanta as he spun and fired inches over soon after.
The Giallorossi did eventually draw level through Cristante, as his long-range strike easily beat goalkeeper Pierluigi Gollini and nestled in the bottom corner.
Dzeko ought to have completed the turnaround late on as he raced clear into the box, but the Bosnian fired at Gollini, whilst the striker headed just over the bar in stoppage time.
Roma substitute Borja Mayoral saw a goalbound shot deflected behind as the hosts pushed for a winner, but ultimately could not find a way through, whilst Ibanez saw two quick yellow cards in stoppage time for cynical fouls and was dismissed.
The draw sees Atalanta move a point behind second-placed AC Milan, whilst Roma remain seventh.