All thee goals at the Al Maktoum Stadium came in the first half. Gabriel began the scoring in the 19th minute with a header from a corner before Eddie Nketiah and Fabio Vieira added quickfire efforts in the 33rd and 39th minutes.
Despite being without 10 players who have been in action with their national teams in Qatar, Mikel Arteta fielded his strongest possible lineup from those players remaining. Captain Martin Odegaard, winger Reiss Nelson and midfielders Mohamed Elneny and Sambi Lokonga also started in front of a back four of Cedric, Gabriel, Rob Holding and Kieran Tierney.
Lyon's lineup under former France coach Laurent Blanc featured ex-Arsenal striker Alexandre Lacazette but the 31-year-old failed to find the net against his former employers before being taken off in the second half.
Both teams made wholesale changes in the second half, with Arteta calling on several members of Arsenal's under-21 side, though there were not further goals.
As part of the Dubai Super Cup, a penalty shootout took place after full-time, with Arsenal winning 2-1 thanks to three saves from goalkeeper Karl Hein to pick up an extra point.
"It was our first game here since I've been a manager and it was a great experience," Arteta said. "Thank you so much to everybody involved for making this possible. I'm really happy because we won and played at a good level."
Arsenal will be without Gabriel Jesus when competitive action returns after the striker underwent knee surgery following an injury suffered in Brazil's World Cup group-stage match against Cameroon. While no official timetable for his return has been set, sources told ESPN that he is likely to be sidelined for around three months.
"We know that he needed some intervention in the knee," Arteta said after the win over Lyon. "We'll have to take it day by day, week by week and see [where] it takes us."
On the question of whether Arsenal will seek a replacement in the January transfer window, Arteta added: "What it affects is who we are as a team because he gives us so much, so what we can do after that, when we know the timescale [of his recovery] and when we can have him back, we will look at the options and try to make the right decision."