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City secured victory thanks to Ghanaian forward Antoine Semenyo, who scored the only goal of the match in the 72nd minute with a backheel finish.
The win handed the side managed by Pep Guardiola their second title of the season.
Manchester City had already won the EFL Cup earlier this season, beating Arsenal F.C. in the final.
City are also competing with Arsenal for the Premier League title, sitting second in the standings, two points behind the London club, with two rounds remaining.
Despite fatigue from a demanding season, Manchester City managed to overcome Chelsea, who failed to rescue a difficult campaign or secure continental qualification by winning the FA Cup.
Chelsea currently occupy ninth place in the Premier League table.