Ahmed Elhmohamady's own-goal, just after the half-hour mark, gave Pep Guardiola's team a lead at the interval, before they pressed home their advantage.
Aguero squeezed in a second goal three minutes after half-time, set up by Raheem Sterling, who also created the third with a short pass that Fabian Delph thumped in for his first league goal of the season.
Victory strengthened City's grip on the fourth and final Champions League qualification spot, with Guardiola's men now seven points ahead of fifth-placed Arsenal
Meanwhile Hull remained just above the relegation zone.
Hull's home form has been the key factor in their push for top-flight survival since manager Marco Silva’s arrival in January; they arrived at the Etihad having taken just one point from their previous 13 away matches.
Silva set up his team to absorb City pressure and then cause problems on the counter-attack, which they did at times, without causing Bravo too many difficulties for most of the match.
The Chile international was recalled in goal for his first Premier League appearance since January 21, but all he had to do in the first half was punch away one cross from Kamil Grosicki.
- Sterling service -
Jakupovic was untroubled by three long-range City efforts, one from Aguero and two from Delph, all of which were off target.
The goalkeeper, though, needed to be on his toes to tip over a free-kick from Yaya Toure, moments after the midfielder, set up by Delph, had steered a first-time shot that dipped just over.
City's probing brought reward just after the half-hour mark, when Jesus Navas, converted from a winger into a right-back, whipped over a cross on the run that eluded Aguero and was turned into his own net by Elmohamady.
Hull should have equalised immediately as Grosicki cut back from the left for Evandro to steer a cross-shot goalwards, but Oumar Niasse lost his bearings and skewed his effort sideways from seven yards out.
Silva, making his 300th appearance for City, volleyed over from Sterling's cross on the stretch just before half-time.
But the home side did extend their lead three minutes after the interval, as Sterling darted down the right and cut across goal for Argentina international Aguero to control and squeeze a shot past Jakupovic, Elmohamady and Michael Dawson as they tried to block.
Sane almost added a third instantly, but fired Sterling's cross on the run straight at the goalkeeper.
That third goal arrived just beyond the hour mark, as Sterling raced on to Toure's pass to lead another counter-attack, and then rolled a pass left for Delph to thump in his first Premier League goal in more than a year.
That would have made it a perfect afternoon for Guardiola, but it was spoilt late on as Shaun Maloney cut the ball back for Ranocchia, on loan from Inter Milan, to steer a shot under Bravo's dive with the visitors' only effort on target.