With Sunday's La Liga Clasico against Real Madrid looming, Barca are also left with concerns over defender Gerard Pique, who limped off with an injury after falling heavily on his ankle.
Formula One champion Lewis Hamilton and Barcelona forward Lionel Messi are declared joint winners of the Laureus World Sportsman of the Year Award in Berlin.
The victory took Barcelona level on 52 points with Real Madrid, who lead the Spanish league standings on goal difference and host Celta Vigo on Sunday. Getafe stay third on 42.
Antoine Griezmann and Clement Lenglet scored first-half goals before Lionel Messi netted two and Arthur added another after the break as Barcelona reached the last eight of the Copa for the 10th straight year.
A mistake by Barca's usually excellent goalkeeper Marc-Andre ter Stegen gave the home team an equalising goal that sealed the match.
Now aged 32, it's Messi's first Ballon d'Or since 2015 and his sixth overall as he moves one ahead of his old rival Cristiano Ronaldo.
Messi's strike saw Barca return to the top of the standings with 31 points after 14 games, ahead of Real Madrid on goal difference, while Atletico were left in sixth spot on 25 points, having played one match more than the two pacesetters.
Suarez put Barca in front in the 29th minute before setting up Messi on his landmark night moments later.
Lionel Messi scored two goals and set up two more as Barcelona extended its winning streak and regained the Spanish league lead by comfortably defeating Valladolid 5-1.
The Catalan striker thrust his finger in the air before pumping his fist in celebration after scoring in the 78th minute. Messi had gone scoreless in his previous four appearances after being sidelined for five games with injuries.
The Argentinian playmaker's withdrawal will be a major concern for Barca, particularly given this was Messi's first start of the season after just recovering from a niggling calf injury sustained at the start of August.
Megan Rapinoe was rewarded for leading the US to women's World Cup title while Lionel Messi moves one ahead of Cristiano Ronaldo.
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