All the goals came in the second period as Koke, Mario Mandzukic, Antoine Griezmann, Diego Godin and Alessio Cerci secured a valuable three points for the Spanish champions.
Olympiacos are top of Group A after former Fulham midfielder Pajtim Kasami grabbed the winner in a 1-0 victory over Juventus.
The Greek champions are level on points with Atletico.
Giulio Donati and Kyriakos Papadopoulos both scored in the second half as Bayer Leverkusen beat Zenit St Petersburg 2-0 to take charge of Group C.
Monaco climbed above Andre Villas-Boas’ side into second place as they drew 0-0 with Benfica, who earned their first point of the campaign.
Borussia Dortmund hammered Galatasaray 4-0 away from home to make it three wins out of three in Group D.
Pierre-Emerick Aubameyang scored twice in 18 minutes for the visitors, first tapping home Marco Reus’ pin-point pass before adding another from close range.
Reus added a third before half-time with a stunning, curling shot before substitute Adrian Ramos scored a fourth late on.
Yordan Minev’s last-gasp strike lifted Ludogorets to a famous Champions League victory over 10-man Basle. The full-back fired low into the net from distance in the first minute of stoppage time to give his side a 1-0 triumph and ensure they became the first side from Bulgaria to take a point in the group stage of Europe’s elite club competition.
Ludogorets are now level on points with Group B rivals Liverpool and Basle.