A New York Times investigation accused the site of being "infested" with child-abuse and rape-related videos.
Pornhub, which has denied the claims, called Mastercard's actions "exceptionally disappointing".
Fellow payments giant Visa has suspended use of its cards on the site pending the outcome of its own review.
Mastercard launched its inquiry after Pulitzer Prize-winning journalist Nicholas Kristof named it in his New York Times article, saying he "didn't see why search engines, banks or credit-card companies" should "bolster" Pornhub.
