The Italian side took the lead in Italy after just 12 minutes.
Ronaldo ensured that the two teams would go into the half-time break level as he found the net in added time.
United fell behind once again when Duvan Zapata broke the offside trap and finished past David de Gea 11 minutes after half-time.
The Red Devils struggled to find an equaliser and were still behind going into stoppage time.
But Ronaldo popped up with a brilliant leveller to ensure his side came away with a share of the spoils.
The ball found its way to the 36-year-old just outside the box and he drilled a lovely effort that found its way to the corner of the net.
Paul Merson was covering the game on Sky Sports and he went wild when the United striker found the net.
He started: "Ronaldo has got the ball, just on the edge of the box. Trying to make space. Still there. All of a sudden to Ronaldo... volley... what a goal! Oh my Ronaldo! He's just scored... out of absolutely nothing!
"It's come to him and he;s hit a right footed volley and it's gone into the corner. Unbelievable."
He continued: "I don't know how he hasn't pulled his thigh because he hasn't touched the ball. He's got to be one of the best finishers ever.
"It comes to him and he volleys it. It's just out of nothing. And he hits across it into the far corner. What a goal. What a goal. And what a point for United."
Merson said later on, per Sky Sports: "He didn't touch the ball in the second half. Not through his fault, he just didn't get the service. But it comes to him and there's no snatching at it, he hits through the ball perfectly.
"It's absolutely phenomenal and his first goal was brilliant as well.
Atalanta 2-2 Manchester United Reaction Show | The Football Terrace
"I was one of the big critics. I was one who wasn't sure about him coming back. But if you give him chances, he will score goals. Thirty-six or 46, it doesn't make any difference, he will finish.
"If you took away his two goals tonight, he's a two out of 10. But his two goals are phenomenal and I'm lost for words."
United now know a win against Villarreal in their next group game could be enough to see them qualify for the knockout rounds.