An injury to midfielder Yaya Toure late on may yet cause City some headaches but manager Manuel Pellegrini was delighted with the attitude of his side.
"A big team must always be focused on both competitions," he said.
"Premier League and Champions League. Every big team must do it every year.
"Stoke is fighting for nothing but nobody wants to lose games. It was important to score the first goal."
Fernando opened the scoring on 35 minutes and Aguero converted from the penalty spot just before half-time when Iheanacho was fouled by Ryan Shawcross.
Iheanacho then scored twice in the second half to complete a rout to move City into third place.
"Kelechi Iheanacho is an important young player with a lot of future," Pellegrini said.
"He scores lots of goals but he is not just a penalty box player. I am sure that his role in this team will be very important.
Pellegrini left out defender Vincent Kompany but said his captain would be fit to face Madrid.
"Vincent Kompany is not able to play Saturday and Tuesday at this moment," he said. "We did not want to take the risk."
Stoke are safe in ninth place but have now conceded 12 goals in their last three games. Newcastle's survival hopes looked set to take another blow when they trailed 2-0 at half-time to Liverpool, thanks to goals from Daniel Sturridge and Adam Lallana.
But a vastly-improved second-half display saw Papiss Cisse pull one back and Jack Colback equalise for a vital point.
Newcastle remain second-bottom but are now level on points with third-bottom Sunderland, who host Arsenal on Sunday.
Southampton won 4-2 at relegated Aston Villa thanks to two goals from Dusan Tadic and one each from Sadio Mane and Shane Long.
The Saints are now just one point behind seventh-placed Liverpool, and seven ahead of Chelsea, who moved up to ninth with a 4-1 win at Bournemouth.
Eden Hazard scored his first goals of the season with a pair while Pedro and Willian got the others.
-AAP
