The 17-year-old attacking midfielder impressed throughout the first of Arsenal's three pre-season friendlies in Singapore and showed just why he is one of the club's most talked-about young players when he scored from outside the box early in the second half.
The goal cancelled out Luciano Vietto's opener for Atletico, which was without the likes of Antoine Griezmann, Diego Godin and Jose Gimenez but nevertheless exposed Arsenal's defensive frailties on occasion and looked the better organised of the two teams.
Arsenal's young guns failed to fire in the penalty shoot-out, though, with Joe Willock and Eddie Nketiah missing their spot-kicks along with Henrikh Mkhitaryan as Atletico triumphed 3-1.
Emery gave valuable minutes to new additions Bernd Leno and Sokratis Papastathopoulos in a side that blended youth and experience, with Alexandre Lacazette looking sharp as he prepared to continue the good form he enjoyed in 2017-2018.
Atletico, whose first competitive test of the season will come when they face Real Madrid in the UEFA Super Cup on August 15, improved as the game unfolded and were unfortunate not to find a winner as Arsenal's error-prone defence began to tire.
Playing a similar system to that employed primarily by Arsene Wenger last season, Arsenal started with Aaron Ramsey and new signing Matteo Guendouzi protecting the defence as Lacazette spearheaded a front four featuring young attackers Reiss Nelson and Smith Rowe.
Nelson sped to the by-line after four minutes and crossed to the far post but couldn't quite pick out Pierre-Emerick Aubameyang, who sliced a shot wide from a deep Smith Rowe corner moments later as Arsenal looked dangerous early on.
Having started slowly, Diego Simeone's under-strength Atletico team came to life when Juanfran burst into the box just before the half-hour mark and pulled the ball back to Angel Correa, whose first-time shot was headed clear by Shkodran Mustafi.
Ramsey threaded a pass in behind the Atletico defence where Lacazette thumped the ball onto the palms of the alert Jan Oblak, who was tested again when the French forward played a neat one-two with Smith Rowe and tried another low shot.
Having dominated the first half, Arsenal were undone four minutes before the break when Correa turned Rob Holding and crossed to the unmarked Vietto, whose diving header from the right side of the box found the far corner of the net before Leno could react.
The second half was just two minutes old when Smith Rowe picked the ball up 30 yards from goal and jinked his way between two defenders and drove the ball into the top right corner of the net with a confidence that cannot have failed to impress the watching Emery.
In contrast to their fluency going forward, Arsenal looked edgy and unsure of themselves in defence and Atletico should have restored their lead when Guendouzi failed to clear the ball in the six-yard box but Joaquin Munoz fired over the bar from point-blank range.
Emery sent on Sokratis as he made mass second-half substitutions, with Calum Chambers and Mkhitaryan also featuring in the last half hour as the game lost its shape.
The last of Arsenal's chances fell to young forward Nketiah, who burst down the right flank and flashed a shot across the face of goal but his effort was saved by Antonio Adan as Atletico held firm.
Adan then starred in the shoot-out, saving from Mkhitaryan, Willock and Nketiah before taking the winning kick himself and burying it in the top right corner of the net.