The Championship side were no match for the Barclays Premier League champions, who responded to last week's title setback with a dominant display at the Etihad Stadium.
Yaya Toure began the procession early on before Aguero added a penalty and a fine finish either side of a close-range Carlos Tevez effort.
Manchester City reached the FA Cup quarter-finals with a 4-0 victory over Leeds on Sunday. Arouna Kone scored a goal towards the end of each half as Wigan hammered Huddersfield 4-1 at the John Smith's Stadium to reach the quarter-finals.
After a quiet opening, Wigan took the lead through the impressive Callum McManaman before Kone increased the advantage five minutes before the break.
James McArthur scored a stunning third for Wigan and, after Lee Novak had pulled a goal back for Huddersfield, Kone seized on a defensive error to score a late fourth.
In a fourth-round replay, Frank Lampard and John Terry both scored as holders Chelsea beat Brentford 4-0 in a replay at Stamford Bridge to set up a fifth-round clash with Middlesbrough.
Juan Mata fired a clinical opening goal after 54 minutes and Oscar, who hit the outside of a post in the first half, tucked in his second goal in four days after 68 minutes.
Mata was the provider for Lampard's 199th Chelsea goal before Terry headed in an 81st-minute fourth as last season's Champions League winners stayed on course for a fifth FA Cup triumph in seven seasons.
Source: Manchester City MAD