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.
Lionel Messi came on as a substitute for the last 30 minutes for his first appearance of the season but was unable to spark the visitors' struggling attack, with Dortmund creating the best chances of the game.
Lionel Messi and Argentina can still appeal the decision, which stops the striker from playing in four friendlies this year.
Brazil advanced to the final of the Copa America with a 2-0 win over old rivals Argentina in Belo Horizonte thanks to a goal in each half from Gabriel Jesus and Roberto Firmino.
Barcelona Vice President Jordi Cardoner, however, denied the Spanish soccer club was in contact with Neymar amid reports the Brazil striker wants to leave Paris Saint-Germain.
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