United coach Ole Gunnar Solskjaer’s knives went down when his side were 2-0 down at halftime at Old Trafford, Mario Pasalic and Turkish center-back Merih Demiral scored for Atalanta.
However, Marcus Rashford made up for missing a glorious opportunity just before the break by retracting a goal eight minutes into the second half and sparking another notable comeback.
In their last Champions League game three weeks ago, United fell back at home against Villarreal, but won back 2-1, with Ronaldo scoring the decisive goal in stoppage time.
This time captain Harry Maguire equalized in the 75th minute, Ronaldo headed a Luke Shaw cross to make it 3-2, nine minutes from the end for his record-breaking 137th Champions League goal.
“We have a habit of doing that at this club,” said Solskjaer of another success from behind.
United are now at the top of Group F, two points ahead of Atalanta and Villarreal, who won 4-1 at Young Boys in Bern.
Yeremi Pino gave Villarreal the early lead on his 19th birthday before Gerard Moreno headed the ball to make it 2-0.
Meschack Elia, the Congolese striker, withdrew for the Swiss champions in the 77th minute, but late goals from Alberto Moreno and Samu Chukwueze sealed last year’s Europa League winner’s victory.
After losing to Juventus last time, Chelsea got their trophy defense back on track when Jorginho scored two penalties in a 4-0 win over Malmo in the rain at Stamford Bridge.
Their evening was marred, however, by an injury from Romelu Lukaku, who won the evening’s first penalty midway through the first half after being injured.
Andreas Christensen had previously put Chelsea in the lead. Kai Havertz scored Chelsea’s second goal, but Timo Werner also had to quit for Thomas Tuchel’s team before the break.
“We have a twisted ankle for Romelu and a muscle and thigh injury for Timo, so they will probably be out for a few days,” said Tuchel.
“We have a lot of games so now we have to find solutions, not excuses.”
Chelsea are second in Group H but Juventus are in the lead with three out of three wins after substitute Dejan Kulusevski scored a 1-0 win over Zenit St Petersburg in Russia with a late header.
Bayern scored four goals in the last 20 minutes to beat Benfica 4-0 in Lisbon and hold a 100 percent record in Group E.
The German champions saw Robert Lewandowski and Thomas Mueller goals not being recognized before Leroy Sane gave them the lead with a free kick at the Estadio da Luz, the site of their victory over Paris Saint-Germain in the 2020 final.
An Everton own goal was followed by a Lewandowski goal and another Sane goal when Benfica were brought back on the ground after beating Barcelona 3-0 last month.
“It’s clear to see how hungry we are, that’s one of our greatest strengths,” Sane told the DAZN broadcaster. Bayern have scored 12 goals without conceding in Europe this season.
Barcelona boosted their own hopes for the round of 16 when Gerard Pique’s first-half goal was enough to beat Dynamo Kiev 1-0 at home in front of a half-empty Camp Nou and scoop first points in the group.
The Austrian champions Red Bull Salzburg are four points ahead of Group G after their 3-1 win over Wolfsburg.
Karim Adeyemi’s early start for Salzburg was soon made up for by Lukas Nmecha, but a double from Swiss Noah Okafor in the second half gave the hosts the points.
Despite their third draw in a row, Sevilla are second, 0-0 at Lille, which have now played 20 games without a win in the Champions League.