The 36-year-old Ronaldo has now scored five goals in four games for United in this season's European campaign and has nine in 11 outings for the club this season.
His outstanding finishing secured a vital point for United, who were minutes away from slipping to third in the group but instead are top on seven points.
Ronaldo hailed the draw as a "good result" and said United were rewarded for their perseverance.
Atalanta took a 12th-minute lead when striker Duvan Zapata cut in from the left and fed Josip Ilicic and the Slovenian's low drive crept under the body of United keeper David De Gea.
Ole Gunnar Solskjaer was forced to abandon his three-central defenders formation in the 38th minute when France international Raphael Varane suffered a hamstring injury and had to be replaced.
With Eric Bailly starting for the injured Victor Lindelof, United had no choice but to revert to an orthodox four-man defence and they once again struggled in that formation.
But just before the break, the visitors produced a superbly worked goal with a flowing passing move ending with a clever back-heel from Bruno Fernandes to Ronaldo, who buried the chance.
Gian Piero Gasperini's Atalanta were well on top after the break and they restored their advantage in the 56th minute when Zapata broke past Harry Maguire, burst into the box and beat De Gea.
United desperately searched for an equaliser and, right at the death, Ronaldo pounced on a loose ball on the edge of the box and with his trademark technique and precision blasted home a low volley to earn a precious point.
