Pep Guardiola made seven changes to his side, starting with a new-look system of a back-three as the likes of Kevin De Bruyne, Riyad Mahrez and Ilkay Gundogan were all rested while Jesus partnered Aguero in attack.
Fulham had won at Anfield a week ago and in the opening 45 minutes more than held there own, even if goalkeeper Alphonse Areola had to be sharp to deny Ferran Torres from the best opening of the half.
After the interval, however, Scott Parker’s side imploded as City scored three times in 13 minutes to ruthlessly put the game to bed.
First, Stones took advantage of Fulham’s high line to meet a Joao Cancelo free-kick and turn home before Jesus capitalised on a defensive mix-up to round Areola and make it two.
More sloppiness in possession cost City soon after as Tosin Adarabioyo – playing against his former club – was robbed by Torres and then fouled the Spaniard in his attempt to recover. Aguero stepped up to bury the resulting spot-kick.
The result extends City’s lead at the top of the table to 17 points with just eight games to play, though second-placed Manchester United have two games in hand.
Fulham, meanwhile, remain in the relegation zone in 18th, level on points with Brighton above them but with a significantly poorer goal difference and having played two games more.