Stones, 22, was replaced after just 18 minutes during the 3-0 win over Hull City on Boxing Day after picking up a knee injury. The England international has however been passed fit for the trip to Anfield, although fellow defender Vincent Kompany remains sidelined with a knee injury suffered in the win over Crystal Palace back in November.
Leroy Sane also remains unavailable having failed to recover from the knock that ruled him out of the win at the KCOM Stadium, but Pep Guardiola's side will be bolstered by the return of their top scorer Aguero, who has completed his four-match ban following his second red card of the season.
"John is much, much better," Guardiola told a press conference. "Vincent and Leroy I think will not be available to play.
"Aguero is ready — he came back good from Argentina. Finally, he came back after four games ban and we are happy he is back."
Ilkay Gundogan is City's only other absentee, with the Germany international set for a long spell on the sidelines after tearing the cruciate ligaments in his right knee.
Liverpool meanwhile will be without midfielder Philippe Coutinho, who has missed the club's last six games after suffering an ankle injury against Sunderland in early December. Joel Matip will also miss out having failed to recover from an ankle injury.
Jurgen Klopp's side currently sit in second place, six points behind Premier League leaders Chelsea. Man City are a point further behind in third place and can leapfrog Liverpool with a win on Merseyside on New Year's Eve.