The Atalanta earned a series of chances later, but poor finishing let them down. Atalanta's task was made harder after Gosens collected his second yellow card after trampling on Jordan Veretout.
Madrid had reached the semifinals or better in eight straight seasons between 2010-11 and 2017-18 before losing to Ajax in the last 16 in 2019 and to Manchester City last season.
Madrid entered the game as the big favorite despite a slew of injuries, and Atalanta's chances diminished further when midfielder Remo Freuler was sent off.
Liverpool registered a dominating 5-0 win over Atalanta in the Champions League here on Wednesday.
"Ronaldo carried out a check with a diagnostic test (swab) for Covid-19. The exam provided a negative result," the Italian champions said in a statement.
The only possible exemption would be a club which has an active outbreak of Covid-19 with more than 10 new positive cases in a week.
A straight knockout final tournament held in one place, akin to a World Cup or European Championship, was the only solution available to UEFA in order to complete its most lucrative club competition, suspended for five months from March until last weekend.
Currently, the club is preparing for the Coupe de la Ligue final against Lyon, slated to take place on Saturday.
Juventus have already sealed their ninth straight league title, but three teams are fighting for second spot -- Inter Milan, Atalanta and Lazio -- going into the last round of matches in Italy.
A Romelu Lukaku header hit the woodwork after 18 minutes with Alexis Sanchez also missing a chance for the winner just after the break.
Muriel struck just after an hour as Atalanta extended their unbeaten run to 15 games to move six points behind Juventus, and two ahead of third-placed Inter Milan.
Gian Piero Gasperini's side extended their unbeaten league run to 13 games to move six points behind leaders Juventus who visit eighth-placed Sassuolo on Wednesday.
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