Daniel Rios scored in the fifth minute for Charlotte (11-17-2, 35 points), who ended a three-game losing streak. Charlotte FC are only 3-7-0 in their past 10 matches, but still have a chance at reaching the playoffs in their first MLS season.
Though NYCFC (13-11-7, 46 points) had plenty of opportunity with the man advantage, NYCFC had only one shot on goal in the game lacked quality chances both before and after Fuchs' red card.
Charlotte FC became the first expansion team in league history to sweep a season series against a defending MLS Cup champion. Charlotte also collected a 3-1 road victory at New York City on Aug. 17.
Both losses to Charlotte have come within a dismal 1-7-2 stretch for New York City FC. Fatigue could be a factor for NYCFC, as Saturday marked the team's eighth game in 29 days.
Coming off consecutive shutout losses, it took Charlotte FC just five minutes to find the net on Saturday. Off a throw-in, Karol Swiderski sent a cross into the center of the box, and Rios connected with a header for the forward's second goal of the season.
Rios' tally was one of three early chances for Charlotte, who dominated the opening 15 minutes. Brandt Bronico chipped a shot off-target following a long downfield pass from Swiderski, and just moments before Rios' goal, Adilson Malanda hit the goalpost on a close-range header.
Kamil Jozwiak also hit the post early in the second half, following a NYCFC turnover.
Charlotte goalkeeper Kristijan Kahlina recorded his seventh shutout of the season.