Arsenal teenager Emile Smith-Rowe cancelled out Luciano Vietto's opener to take the game to a shootout.
The win means Atletico now occupies the 7th position on the log with 3 points from one game, while the Gunners occupies the 9th position with no point from one game.
Arsenal will be given permission by Sevilla to sign midfielder Steven Nzonzi from the Spanish club, provided the Gunners are prepared to meet his £36m release clause.
Both sides fielded unfamiliar line-ups but Arsenal were dominant in the first half before they were hit with a sucker-punch four minutes from the break.
'For me, I want him to stay with us, to work with us, to give the team the big performance.
Signed for a reported £7 million (S$12.5 million) from French club Lorient earlier this month, the 19-year-old was forceful in the hustle and bustle of midfield as he showed no fear in asking for the ball from his established team-mates.
Emery was appointed as Arsenal head coach in May
Wenger's longevity makes a coaching change at Arsenal much more momentous than it would be at nearly any other club, and so the question about how the new manager might change the club take on even more importance.
For that, I am happy with his work today, not only today but every day.
Atleti's first-choice keeper Jan Oblak made three excellent first-half saves but they took the lead against the run of play when Vietto headed in a fine cross, giving new £19m keeper Leno no chance.
The Gunners and Atletico will stay in Singapore for the rest of July to play one more match.
Rowe, who turns 18 tomorrow, slalomed his way into the heart of Atletico's defence in the 47th minute before firing a fierce shot into the top corner, a strike that had Arsenal coach Unai Emery purring.
"I think this is the moment for the young players to show quality like Emile did", he added.
"It's every day. He's starting today's match because his performances have been good in every training session". "Aaron is an important player for us".