Ryan McGivern and Shaun Wright-Phillips were on target in the first half for Roberto Mancini's team in front of 11,250 fans at AT&T Park.
Summer signings Stefan Savic and Gael Clichy were handed debuts along with Swiss youngster Freddie Veseli in an unfamiliar starting line-up.
Northern Ireland defender McGivern opened the scoring after 17 minutes, pouncing on the loose ball and curling home a neat finish after Edin Dzeko's effort had been cleared.
Ten minutes later, City had their second. Wright-Phillips, who had set up Dzeko in the build-up to the first goal, picked up possession outside the box and lashed a low drive into the bottom-right corner.
Of the team that played in the first half, only Vladimir Weiss remained on the pitch after the interval as Mancini made 10 changes to give the rest of his squad a run-out.
John Guidetti struck the post in the final minute but there was to be no third goal.
City continue their preparations for the new campaign with a game against Vancouver Whitecaps on Monday.