Columbus took the lead in the 10th minute when Federico Higuain netted his seventh goal of the season.
Villa was linking up well with Andrea Pirlo and the Spaniard's volley was saved in the bottom right corner.
New York were level in the 29th minute when Andrew Jacobson struck after a passing move got the better of the Columbus defence.
It took until the 61st minute for either team to threaten again, and it was Villa who forced Clark into another save.
It was Meram who scored the winner late on, grabbing his fourth goal of the season to ensure Columbus would travel home with the three points.