The injured trio's return is well timed for Roberto Mancini as City look to hold off a charge from Chelsea and Tottenham for an automatic Champions League group-stage spot.
The three City players have not played together in the same team under Mancini since the defending champions' beat Stoke 3-0 on New Year's Day.
The return of club captain Vincent Kompany in particular is a huge boost for the club. The Belgian has been out with a calf problem for the past two months, and City have dropped points to Liverpool, Southampton, and Everton in his absence.
A knee complaint has kept Aguero on the sidelines since the end of February.
Yaya Toure missed the 2-0 loss to Everton with a migraine, but all should return for the visit of Alan Pardew's Newcastle to the Etihad Stadium this weekend.
The top three teams in the Premier League qualify automatically for next year's Champions League, and with Chelsea and Spurs in hot pursuit, City face a battle to hold on to the second spot.
The Stamford Bridge club have moved to within four points of Roberto Mancini's side, while Spurs are just one point further back.
The fourth-placed Premier League side must enter the Champions League at the pre-qualifying stage in August, a month before the group stages kick off.
The big games left for City this season include a trip to Old Trafford to face Manchester United on April 8 and to White Hart Lane to play Tottenham two weeks later on April 21.