Riding high at the top of the Premier League and unbeaten in Europe, the Gunners controlled the tempo early on. Eberechi Eze came close to breaking the deadlock when his strike deflected off David Hancko and hit the crossbar, with Declan Rice firing the follow-up over.
A nervy moment followed as goalkeeper David Raya delayed a clearance, allowing Julian Alvarez's long-range shot to drift just wide for Atletico.
The visitors struggled to match Arsenal's intensity, and despite Gabriel Martinelli's first-half goal being disallowed for offside, the Gunners remained dominant. Alvarez nearly gave Atletico the lead when his dipping shot struck the crossbar, but the game remained scoreless at halftime.
The second half saw Arsenal unleash their full force. Just after the break, Gabriel powered home a header from a set-piece to give the hosts a deserved lead.
Moments later, 17-year-old Ethan Nwaneri sparked the second goal, driving forward and finding Martinelli, who curled a precise shot past Jan Oblak.
Viktor Gyokeres then stole the show, ending his goal drought with a deflected strike off Hancko, making it 3-0.
Arsenal's relentless pressure culminated in a fourth goal from another set-piece. Rice's corner was nodded across goal by Gabriel, and Gyokeres bundled in his second, sending the Emirates into raptures with "Ole" chants echoing around the stadium.
Mikel Arteta praised his team's breakthrough, telling Amazon Prime, "It was a really tough match, we knew when it was 0-0 it was going to be really tough, when it was 1-0 they opened up a little bit, (it made) it easier for us to find the spaces, very happy, a big performance."
The victory marked Arsenal's third consecutive clean sheet in the Champions League and their fourth overall, while extending their winning streak against Spanish opposition to seven games. For Atletico, the defeat ended a six-match unbeaten run across all competitions, exposing vulnerabilities despite their earlier 5-1 away win over Eintracht Frankfurt in the competition.
This emphatic display cements Arsenal's credentials as serious contenders in Europe, with their clinical finishing and set-piece prowess proving too much for a shell-shocked Atletico side.
La Liga served up a gripping weekend of twists on Sunday, as Robert Lewandowski's hat-trick inspired Barcelona to a 4-2 victory over Celta Vigo, cutting Real Madrid's lead at the top to just three points after their stalemate at Rayo Vallecano.
Rumours coming out of Spain are suggesting that Real Madrid and Liverpool are considering a swap deal that would see two superstars switch teams.
Arsenal saw their winning run ended by Sunderland, while Chelsea claimed a convincing victory over Wolves in Saturday's Premier League action.
Manchester City forward Omar Marmoush has emphasised the importance of winning against defending Premier League champions Liverpool at the Etihad Stadium on Sunday.
