The Argentina striker bagged a goal in each half to cap a brilliant performance from Pep Guardiola's side, who look in fine shape ahead of next weekend's Premier League opener.
Guardiola named a strong lineup, with six of our World Cup stars in his starting XI.
And with the new Premier League season just a week away, his players will now be much closer to full match sharpness after a dominant display at Wembley.
City were quicker and more inventive than their opponents and were in total control throughout an entertaining afternoon, and the only disappointment was we didn't score more goals.
City started brightly. Riyad Mahrez's early effort from the edge of the area after a couple of stepovers was blocked, before Bernardo Silva, fantastic throughout, flashed a dangerous cross across the face of the six-yard box that no one was there to finish off.
It was a sign if things to come.
Phil Foden, who excelled on the spacious Wembley pitch, fed Aguero on the edge of the 18-yard box. He took one touch with his right to steady himself, before firing past Willy Caballero with his left. It was Aguero at his clinical best and after a seven-moth wait, he had his elusive 200th City goal.
Aguero then slipped Leroy Sane through with a fine pass and the German should have done better, but his first touch was heavy and the ball ran through to Caballero.
In a rare first-half Chelsea attack, Claudio Bravo spilled Callum Hudson-Odoi’s effort from distance, but John Stones was there to hook the ball clear. Stones, continuing where he left off in Russia, looked strong defensively and was supremely comfortable on the ball all afternoon.
In another sweeping City move, Fernandinho dispossessed Alonso and set Bernardo on the charge. The Portuguese playmaker, direct as ever, went at the heart of Chelsea and slipped in Mahrez just inside the area – but his touch let him down and David Luiz was able to get it clear.
Aguero should have had his 201st moments after the half-time break, but after rounding Caballero his effort hit the sidenetting.
City's No. 10, though, can't be kept quiet for long, and he finished off a brilliant breakaway move, started by Stones who won the ball brilliantly on the edge of his own area, to make it 2-0 just before the hour mark.
Caballero's fine reaction stop denied Aguero his hat-trick as City continued to attack Chelsea.
A late scramble inside the penalty area almost saw Chelsea halve the arrears - but Bravo and substitute Nicolas Otamendi somehow scrambled the ball clear to preserve a confidence-boosting clean sheet.
And in added time, Bernardo almost got the goal he deserved but for a goal-line clearance from Anotnio Rudiger.
This was mainly about fitness and preparation ahead of the new season, but Guardiola will have been hugely encouraged by the performance of his players.They were outstanding.
Man of the Match: Bernardo Silva
Bernardo excelled, floating between the lines to find space and do damage to the Chelsea backline.
His energy and enthusiasm saw him pop up in positions all over the pitch, and his touch and technique meant he was consistently effective on the ball.
Vision, passing quality, tenaciousness and ability to control the tempo - he is a fine midfielder.
He played more centrally here than we saw him last season and it's clear he could be occupying that role more often.
Aguero: The deadliest in City history
When Aguero scored away at Napoli back in November, he became the Club’s greatest ever goalscorer, overtaking Eric Brook’s record, which had stood for 78 years.
That was his 178th in a Blue shirt – and now, nine months later, he has reached another significant milestone. His 200 have been amassed in just 293 games.
It’s an incredible record that underlines his predatory instincts and assuredness in front of goal. A genuine Club legend.
Breakdown of his 201 City goals:
147 Right Footed
35 Left Footed
181 Inside Box
19 Outside Box
Reaction: Pep Guardiola
"When you win, you're happy. I want to congratulate the Chelsea players for they did the same effort like us.
"We don't have to think too much about defending the title. That was the first game - we have to prepare game by game.
"In April and May, we will know. The result will show who we are. We're not talking about having to win the Premier League title.
"We have to play with this attitude and what we have done. We'll see at the end of the season what our level was."
City now have a week of training before we open our Premier League campaign with a trip to Arsenal.