"It ran its course," a source tells Us. "They were dancing and working together all the time and then they barely saw each other."
Madonna, 55, and the 25-year-old dancer first began dating in late 2010 after Zaibat performed with Madonna's daughter Lourdes, 17, at the launch of her Macy's clothing line. He went on to work as a backup dancer during the singer's MDNA world tour in 2012.
Though the couple often kept quiet about their relationship, the two were spotted showing off some PDA back in August 2011 while celebrating the "Vogue" singer's birthday in The Hamptons. In May, the pair made their last red carpet appearance together at the Met Gala in NYC.
News of the split comes just weeks after the "Material Girl" singer was photographed reuniting with her ex-husband Sean Penn in Haiti to help with the J/P Haitian Relief Organization following the area's 2010 earthquake. The exes were also joined by Madonna's son Rocco, 13 (her son with her second husband, Guy Ritchie).