The Gunners, armed with a commanding 3-0 lead from the first leg, showcased resilience and clinical finishing to outclass the 15-time champions and set up a blockbuster clash with Paris Saint-Germain.
The visitors weathered early pressure from Real Madrid, who probed but failed to breach Arsenal's resolute defence. A golden opportunity arrived when VAR awarded Arsenal a penalty after Raul Asencio fouled Mikel Merino, but Bukayo Saka's chipped effort was brilliantly saved by Thibaut Courtois.
Real Madrid thought they had a penalty of their own moments later, only for Declan Rice's challenge on Kylian Mbappe to be overturned after review.
After the break, Real Madrid pushed harder, with Mbappe and Vinicius Junior testing Arsenal's resolve.
However, it was Arsenal who struck decisively in the 65th minute. A flowing move saw Merino release Saka, who redeemed his earlier miss with a delicate finish over Courtois, effectively sealing the tie.
Real Madrid responded quickly, as Vinicius capitalised on a William Saliba error to level the score on the night, but the hosts never truly threatened a comeback.
In stoppage time, Gabriel Martinelli capped Arsenal's triumph with a clinical breakaway goal, sparking wild celebrations among the travelling fans. The victory marked Arsenal's 19th progression in 21 UEFA ties after winning the first leg at home.
Mikel Arteta, beaming with pride, described the night as a career highlight. "One of the best moments in my football journey," he said afterwards. "To beat a team with Real's history, in this manner, is something we'll cherish. We believed we could do it, and the players delivered."
Looking ahead to PSG, Arteta acknowledged the challenge. "They're a transformed team, on an incredible run," he said. "But tonight, we celebrate."
Recent updates from Arsenal's official X account hailed Saka's "moment of magic" and Martinelli's "ice-cold finish," while Arteta praised the squad's unity in a post-match press conference, saying, "This group has the heart and hunger to go further."
For Real Madrid, the defeat stings as they turn focus to a crucial La Liga clash with Athletic Club, aiming to close the gap on leaders Barcelona. Arsenal, meanwhile, march confidently towards their first-ever Champions League crown.
Bayer Leverkusen head coach Xabi Alonso has chosen not to comment on growing speculation linking him with a potential return to Real Madrid for next season, insisting that now is not the appropriate time to discuss his future.
Arsenal manager Mikel Arteta has expressed confidence that forward Kai Havertz could make a surprise return from injury before the end of the season, raising hopes that the German international may be available for their UEFA Champions League push.
Arsenal have reportedly cooled their pursuit of Wolverhampton Wanderers' forward Matheus Cunha due to concerns over his on-pitch behaviour, according to recent reports.
Thibaut Courtois hit out at his Real Madrid teammates for "playing too individually" after they were dumped out of the Champions League by Arsenal.
