The Brazilian full-back, who found the net last month against Liverpool, edged out veteran midfielder Paul Scholes to scoop the award.
"I'm very happy to win this award, especially since I found out that defenders never win it," Rafael told the club's official website. "It's just an honour to win, especially to beat Paul Scholes, and I'm very proud.
"It was a good month for me, very consistent, playing many games and of course scoring the goal at Liverpool was the high point for me. I think scoring at Anfield probably helped a lot with the voting."
Rafael is only the third United defender to win the award since its inception back in 2007.