After leading the Villains to a 2-0 win over Wolverhampton Wanderers last Saturday, Emery opted to make five changes to his starting lineup for the clash at the Etihad Stadium, with Clement Lenglet, Lucas Digne, Nicolo Zaniolo, Jhon Duran and Tim Iroegbunam all recalled.
Pau Torres, Alex Moreno, Youri Tielemans, Leon Bailey and Ollie Watkins were the quintet who made way, the latter of whom was ruled out with a hamstring injury.
Emery was then forced to make a sixth change less than an hour before kickoff, as goalkeeper Robin Olsen replaced Emiliano Martinez, who pulled out of the first XI through illness.
Villa held their own against Man City for much of the first half, with Duran slotting home a 20th-minute equaliser to cancel out Rodri's early opener, but Phil Foden inspired the Citizens to a comfortable victory with a superb hat-trick.
Foden scored a free kick on the stroke of half time to put the hosts back in front, before netting twice in quick succession midway through the second half to condemn illa to their eighth league defeat of the season.
Emery defends team selection in Man City defeat
Emery has since confirmed that his decision to rotate his side was with the club's hectic fixture schedule in mind, including Saturday afternoon's home encounter with Brentford followed by a Europa Conference League quarter-final clash with Lille next week.
"The changes were needed, for injured players and because we will need players to give them confidence playing and practicing," Emery said at his post-match press conference.
"We will play a lot of matches in the next weeks, starting with Saturday against Brentford and then against Lille.
"It was important to be intelligent, even playing against Man City. Of course we were preparing trying to win but with some players injured and others suspended, it was getting practice with some players."
Emery issues Martinez, Watkins, Zaniolo update
Emery was questioned about the fitness of Martinez, Watkins and Zaniolo after the match, the latter was taken off on the 77-minute mark in some discomfort.
The Villa boss "thinks [Martinez] is going to recover for Saturday", even though the goalkeeper was "not feeling good" prior to kickoff due to a stomach issue; Zaniolo should also be fit to feature, while Watkins will be assessed ahead of making a potential return.
Asked if Zaniolo was withdrawn due to injury, Emery said: "It's not an important [injury]. Hopefully he will be better for tomorrow and available to play on Saturday".
On Watkins, the Spaniard added: "Tomorrow we will check him, he is getting better for Saturday."
Tyrone Mings, Boubacar Kamara, Emiliano Buendia (all knee), Matty Cash (thigh) and Jacob Ramsey (ankle) all remain sidelined for Villa, but they will be able to welcome back John McGinn against Brentford on Saturday as he has now served a three-match suspension.
Despite defeat against Man City, Villa remain fourth in the Premier League table, although they only sit two points clear of fifth-placed Tottenham Hotspur who have a game in hand.