Ronaldo scored the winning goal in typical Ronaldo fashion - a late header to erupt Old Trafford. The ball from Luke Shaw was sublime and Ronaldo took full advantage.
Fernandes found himself involved again as his cross made its way to Maguire at the back post unmarked. It was a neat finish by the skipper to equalise with 15 minutes to play and from then on, it was one-way traffic and Ronaldo finished it off in style.
Gian Piero Gasperini's side got off to the perfect start when they were two goals to the good after 30 minutes of play. Mario Pašalić and Merih Demiral scored for the visitors. There were boos at half-time, but Ole Gunnar Solskjaer made no changes at the break and ultimately it paid off.
Solskjaer should once again be singing David De Gea's praise as he kept his side in the game with a tremendous double save moments before Maguire equalised. The Spanish goalkeeper is enjoying a fine start to the season and has now saved his side on numerous occasions.
After a horrendous outing in Leicester on the weekend and a gigantic clash with Liverpool still to come on Sunday, it was vital United beat the crafty and brave Italian side - not only for their Champions League group hopes but for the overall mood of the camp.
Story of the game
If there was one way that United fans could show their support for their club legend that is experiencing a tough run of form, they did it. The United faithful in the Stretford End sang 'Ole's at the wheel' for a solid 10 minutes to open the game.
With four defeats in their last seven prior to the encounter with Gasperini's side, Ole Gunnar Solskjaer made three changes to the shock defeat at the King Power last Saturday. One that saw Paul Pogba benched.
After a quarter of an hour, Atalanta led the hosts. A long knock over the top found Luis Muriel who passed it back to Josip Iličić who then found Davide Zappacosta with a wonderful reverse pass. The former Chelsea wing-back made a darting run down the right flank without being picked up. He then zipped in a low driven cross for Pasalic to tap home from inside the six-yard box.
To make matters even worse, Atalanta doubled their lead shortly before the half-hour mark through Demiral. Teun Koopmeiners whipped in the corner-kick and Demiral had the pleasure of competing with nobody in the air. He placed himself perfectly in between Harry Maguire and Luke Shaw - neither of which seemed to want to get off the ground to head clear.
Despite Rashford's effort which struck the bar in injury-time of the first-half, United showed no real evidence to even suggest a comeback was on the cards. Atalanta went into the break two goals to the good.
In the first three minutes of the second half, Fernandes found Ronaldo through on goal but he smashed it straight at Juan Musso - and by his standards, he should have buried it with his eyes closed.
But fear not, Fernandes finally provided a moment of brilliance. His first-time-flicked pass with the outside of the boot was perfectly timed for Rashford to run onto and slot past Musso from a tight angle. It was an exquisite through-ball, which was finished with perfection for Rashford's second in as many games.
Prior to the assist, Fernandes had arguably been United's worst player.
Scott McTominay's volley then struck the post as United started to knock on the Italians' door - Mason Greenwood picked him out.
De Gea kept his side in with a chance of stealing anything from the game after a remarkable double save.
The skipper, Maguire, equalised with a little over 15 minutes to play. Fernandes again provided the cross from deep which zipped through through the 18-yard box to reach the centre-back unmarked at the back post. It was a tidy finish from Maguire to score his first Champions League goal.
And to round it all off...who else but Ronaldo. Shaw picked up the ball on the left flank like he has done so many times in the past and lofted a wonderful ball to the rising sensation that is Ronaldo.
The United forward has come under immense scrutiny in recent days for his lack of pressing and some have even gone so far as to say he worsens this United side. But that was a reminder of his world-class talents and the fact he is inevitable.
In terms of their Champions League group, they were at one point bottom tonight, however, they now top the group but still have to travel to Bergamo (Atalanta) and Villarreal.