Coming into the contest on the back of five successive Premier League wins, Villa came within inches of making a dream start at the Etihad, as Marcus Rashford fired against the post inside 18 seconds.
Having survived that early scare, City quickly settled into the contest and broke the deadlock in the seventh minute, with Bernardo Silva powering a finish beyond the grasp of Emiliano Martinez after good attacking play from Omar Marmoush.
Undeterred by that setback, the visitors were soon given a golden chance to restore parity when VAR deemed Ruben Dias to have fouled Jacob Ramsey in the box.
Having missed two penalties on their last Premier League away outing, Villa handed the responsibility to Rashford, and the Mancunian-born forward sent Stefan Ortega the wrong way to draw Unai Emery’s side level.
Chances continued to flow for both sides with half-time approaching, as Kevin De Bruyne saw a header thwarted by Martinez, while at the other end, Ortega sprinted from his line to deny Rashford.
Determined to extend their six-match unbeaten run across all competitions (W4, D2), City dominated possession at the start of the second half.
Clear-cut opportunities came at a premium, though, with James McAtee drifting an opportunistic lob narrowly wide of the far post.
Despite seeing little of the ball, Villa continued to pose a threat on the break, as Rashford rounded Ortega, only to fire into the side-netting from a tight angle.
The match remained tantalisingly poised heading into the final 20 minutes, with both sides pushing for a crucial winner.
City looked to have run out of ideas as Marmoush saw a well-taken strike ruled out for offside, but the decisive moment finally arrived in the fourth minute of stoppage time when Jeremy Doku’s low delivery was converted by Nunes at the back post.
That goal earned City their ninth home win in 12 matches in 2025, while Villa missed the chance to go four Premier League games unbeaten on the road for the first time since 2008/09.
Flashscore Man of the Match: Bernardo Silva (Manchester City)