The 22-year-old "Baby" hitmaker headed to 1 OAK in New York after his concert in Brooklyn, and was partying in the VIP section when Desiigner's performance allegedly turned rowdy.
Hip-hop newcomer Desiigner got "a little too hyped" as he bounced around the stage, and then invaded the VIP area, where he jumped around and repeatedly "stomped" on Bieber's toes, reported TMZ.
Video footage obtained shows Bieber shoving Desiigner away from him, prompting Kanye West's protege to turn around and apologise.
An eyewitness claimed the "Panda" hitmaker told the singer, "My bad", before completing his set.
Bieber has yet to comment on the incident, which occurred as he tried to unwind following his two-night stint at the Barclays Centre as part of his Purpose World Tour.