Goals from Gyokeres and Declan Rice capped a dominant first half that manager Mikel Arteta hailed as "one of the best" since he took charge in 2019.
"We started exceptionally well," said Arteta. "Two goals, several big chances, and nothing conceded. That first half was a platform - even though we dropped off slightly later.
Gyokeres ended a five-game league drought with the opener from a corner - Arsenal's 12th set-piece goal of the season. Arteta praised the Swedish striker's all-round display:
"His pressing, positioning, link-up - everything was exceptional. It's a shame he felt something muscular."
He was substituted at half-time and is a doubt for Tuesday's Champions League trip to Prague. Zubimendi also went off with a similar issue in the second half.
Scott Parker's side, now five points above the relegation zone, barely tested Arsenal until Florentino Luís' late header and Marcus Edwards' stoppage-time free-kick struck the post. Parker admitted the early set-piece goal hurt his team's confidence.
"We worked hard on defending those situations," he said. "But Arsenal's delivery and movement are top level."
Despite fitness concerns, the victory marked Arsenal's ninth straight win in all competitions - another sign of a team in commanding form.
"We're in a really good moment," Arteta said. "Now we just hope the lads are okay."
Virgil van Dijk has received strong backing from his former Liverpool manager Jurgen Klopp after the Netherlands captain was subjected to sharp criticism from Rafael van der Vaart during the World Cup.
William Saliba has admitted he is not fully fit at the World Cup, but the France defender insists he will continue to play through the pain as Les Bleus push for a place in the knockout stages.
Belgium will be without influential winger Jeremy Doku for their crucial World Cup Group G clash against Iran after illness ruled the Manchester City attacker out of Sunday's encounter at SoFi Stadium.
Tottenham have strengthened Roberto De Zerbi's squad with the signing of Netherlands international Jan Paul van Hecke from Brighton in a deal worth 52 million pounds.
