Kevin De Bruyne celebrates after scoring the second goal at the Etihad Stadium. AP
Both sets of players came together before kick-off to take a knee in protest of racial injustice, as had Aston Villa and Sheffield United players in the first match of the Premier League's 'Project Restart' after a 100-day stoppage due to coronavirus.
But the difference in quality between the two sides showed once City found their groove as a nightmare evening for Arsenal defender David Luiz condemned his side to defeat.
The Brazilian turned Kevin De Bruyne's cross into the path of Raheem Sterling to fire home the opener in first half stoppage time and was then sent off for pulling down Riyad Mahrez.
De Bruyne converted the resulting penalty before Phil Foden added a third in stoppage time.
City's victory closes the gap on Liverpool at the top to 22 points and means the Reds cannot secure the title when they face Everton in the Merseyside derby on Sunday.
A minute's silence before kick-off remembered those to have lost their lives to COVID-19, including City boss Guardiola's mother.
Black Lives Matter was also emblazoned on the back of shirts where the stars names are normally printed, as the players took a knee around the centre circle.
There was little return to normality once the game did kick-off to the hollow ring of an empty stadium as a torrential downpour added to the difficult conditions for the players.
Arsenal manager Mikel Arteta had made a bold team selection on his return to the Etihad, where he spent three-and-a-half years as Guardiola's assistant.
The Spaniard left Alexandre Lacazette and club record signing Nicolas Pepe alongside Luiz on the bench, while Mesut Ozil did not even make the squad despite a temporary rule change to allow nine substitutes on the bench.
However, after a bright opening, Arteta was left in no doubt of the work he has ahead to close the gap between his new employers and his old.
Guardiola had voiced his concerns for players' welfare over the lack of preparation time to get up to full fitness.
But it was Arteta's plan that was undone by two injuries inside 20 minutes as Granit Xhaka and Pablo Mari hobbled off with Luiz replacing the latter.
As City began to turn the screw, only Bernd Leno in the Arsenal goal kept the score down before half-time.
The German saved brilliantly from David Silva and Riyad Mahrez before Sterling dinked a glorious chance over.
However, the England international made amends when Luiz failed to cut out De Bruyne's cross and Sterling rifled home his first goal of 2020.
Five minutes into the second-half, Arsenal's tough task became an impossible one as Luiz pulled down Mahrez inside the box and was shown a red card.
De Bruyne coolly sent Leno the wrong way from the penalty spot to end the game as a contest and both sides then settled to reserve their energies ahead of a gruelling schedule over the next month.
Yet, there was one more serious looking injury to come as City defender Eric Garcia was stretchered from the field after being wiped out by his own goalkeeper Ederson leading to 11 minutes of added time.
City used the extra time to add a third as substitute Foden side-footed home after Sergio Aguero struck the post.
Defeat is another blow for Arsenal's hopes of a return to the Champions League next season as they remain in ninth, eight points off the top four and five adrift of Manchester United in fifth.
City's place in next season's Champions League will depend on the outcome of their appeal against a two-season ban from European competitions to the Court of Arbitration for Sport.
The appeal was heard last week with a ruling expected early next month.
Arsenal’s game at Manchester City on Wednesday was postponed after players from the London club were put into quarantine, making it the first Premier League football fixture
“I told my wife I’m going to play a little longer,” De Bruyne, 28, said in a live video on his Instagram page. “After this lockdown, I cannot stay at home. I told her I’m going to take two years more.
Gundogan broke the deadlock in the seventh minute, Torres added one more five minutes later 12 to extend the lead.
Manchester United moved within eight points of Premier League leaders Manchester City as Mason Greenwood’s double inspired a 3-1 win over Burnley, while Eddie Nketiah’s last-gasp goal gave Arsenal a 1-1 draw against struggling Fulham on Sunday.
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