The Brazilian had missed five successive matches for the North London club owing to the hamstring injury that he sustained against Everton last month and did not train before Tuesday's Champions League loss to Lens.
With Bukayo Saka also damaging his hamstring at the Stade Bollaert-Delelis, Arteta was at risk of being without both of his first-choice wingers for the visit of the treble winners, but Martinelli was unexpectedly given the green light to make the bench.
Leandro Trossard, Eddie Nketiah and Gabriel Jesus started as Arsenal's attacking trident, but the former also fell victim to a hamstring issue midway through the first half, which saw Martinelli emerge for the second 45 at the Emirates.
Despite his recent layoff, the 22-year-old was as lively as ever on the left-hand side, and with 86 minutes gone, his first-time strike took a wicked deflection off of Nathan Ake's face and nestled into the back of the net.
A Rodri and Kevin De Bruyne-less Man City lacked a cutting edge in the final third throughout the game and could not muster up a late response to Martinelli's fortuitous strike, which gave Arsenal their first Premier League win over the champions since 2015 and ended the Gunners' 12-game top-flight losing run against the Citizens.
Speaking to reporters in his post-game press conference, Arteta detailed how the club's medical team warned Martinelli that Sunday's game would come too soon for him, but his "joy of a kid" mentality ultimately won out.
"He's been saying for a few weeks that I was going to be there for City. Obviously, we were saying that Gabi it would be too early for you, and yesterday he said, boss I told you, I'm going to be ready for this," Arteta said, as quoted by arsenal.com.
"And it happened after 30 minutes that Leo felt something in his hamstring. So, when I turned around, he was already ready, to go with his kit, and saying 'boss, I'm ready to go'.
"He's just got the joy of a kid, his mentality is incredible at his age, and it's just a joy to have him because today he could change the game and he was really helpful for us to win."
Prior to Martinelli's dramatic late winner, Sunday's headline match was an otherwise tame affair and was devoid of any real talking points, although Man City midfielder Mateo Kovacic was highly fortunate to still be on the pitch in the first half.
The Croatian picked up a yellow card for a poorly-timed challenge on Martin Odegaard, catching the Arsenal captain on the studs with his ankle, but VAR official John Brooks saw no reason to upgrade his punishment.
Only a few minutes later, Kovacic was equally late on Declan Rice, but Michael Oliver immediately indicated that he would not be brandishing a second yellow card, much to the chagrin and confusion of the Arsenal players and supporters.
Arteta was loath to discuss the incident afterwards, though, saying: "When I saw the action live, it looked like a big challenge but I haven't seen the replay and I just want to enjoy the win, I hear we will talk about it and understand we have to do something about it but thankfully we managed to win the game."
Arsenal have risen above Man City into second place in the table thanks to Sunday's statement win - behind leaders and arch-rivals Tottenham Hotspur on goal difference heading into the international break, after which they travel to Chelsea on October 21.