However Pep Guardiola's men brushed off a sluggish start and began to go through the gears with Sterling somehow failing to touch in a Leroy Sane cross.
Petr Cech saved well from De Bruyne but City managed to keep the ball alive and soon the ball was back at the Belgian's feet.
Arsene Wenger has a dig at officials after Arsenal lose at Manchester City
This time he swapped passes with Fernandinho before unleashing a low shot beyond the grasp of the Gunners keeper.
It was City's 50th goal of the season - and we are only at Bonfire Night.
Arsenal could have caved in but were let off the hook as Sterling broke clear but fluffed his cross for Sane completely.
And right on half-time they could have gone level as Aaron Ramsey was denied by a smart low save from Eederson Moraes.
There was much to ponder for Arsene Wenger at the break but within five minutes of the re-start his team were further behind.
Nacho Monreal stepped across Sterling as he burst into the box and referee Michael Oliver pointed to the spot.
Aguero - who had ditched the golden boots at half-time - fired the penalty home off the inside of the post - his 179th goal for City.
Ederson was almost embarrassed when he spilled a long-range effort from Iwobi before being bundled over the line by Ramsey.
Is this a penalty for Manchester City's Raheem Sterling or a harsh call on Arsenal's Nacho Monreal?
However he was well beaten soon afterwards when Ramsey slipped through sub Alexandre Lacazette down the right and he rifled a low shot under the keeper.
Wenger's decision to leave the £50 million forward out had Gunners fans scratching their heads and he had scored within eight minutes of coming on.
City could have restored their two goal lead minutes later but Cech did brilliantly to smother from sub Gabriel Jesus.
But the Brazilian did make the points safe in controversial fashion when David Silva found space down the right - when he should have been flagged offside.
He pulled the ball back for Jesus to tap home from close range.
Manchester City's Kevin De Bruyne scores cracking goal against Arsenal at the second attempt
Not having all this about ‘it’s a tight one so benefit of the doubt’. Off is off. This is off, and bursts Arsenal’s bubble at a crucial time. Game over. pic.twitter.com/VgO0ePcecc
Manchester City goalscorer Kevin De Bruyne said: "We know Arsenal are a quality side but I think we contained them quite well. We created more chances and the third goal came at a good time. We should also have scored the second one in the first half. We kept our composure well and it is a great win for us.
"Obviously, it was great to score as it put us ahead and it's always nice every time you score. Maybe we got the benefit from the referee but the penalty was the second one of its type in the game. He had to give a penalty.
"The more you win, the more other teams want to beat you. It's been a great start for us so let's see what other games bring."
Arsenal goalscorer Petr Cech said: "At 2-1 we got back into the game and we were in it, we had time to search for the equaliser but the third goal makes a huge difference.
"I can't comment on the penalty because of my angle, but the third goal, I was surprised. David Silva looked far behind everybody but the referee has a better view than me.
"Referees have a difficult job to do. I don't know if he got it right or wrong but that goal made the difference."
Weekend Round-Up: Watch action from Saturday and Sunday's games in the Premier League