A ten-man Kansas City handed the Premiership club their first defeat on their pre-season North America tour.
Chhetri, who is with the first team since joining the club prior to the 2010 season, made a second-half appearance in the match, replacing Teal Bunbury in the 69th minute. He had two shots on goal in 21 minutes of action.
Despite having Jimmy Conrad controversially sent off late in the first half for a harsh tackle, the home team held on to record a memorable victory over their far more illustrious opponents.
India's captain Baichung Bhutia was the first from the country to play against Manchester United, in 2001 when he was with English Championship side FC Bury.