Rafferty made 10 of 13 shots. He added five steals.
The Paladins posted a season-high 10 blocks.
Isaiah Miller had 16 points and six rebounds for the Spartans (22-4, 11-2), whose eight-game win streak ended with the loss. Demetrius Troy added 13 points. James Dickey had 12 points, nine rebounds and four blocks.
The Paladins evened the season series against the Spartans with the win. UNC Greensboro defeated Furman 89-79 on Jan. 12. Furman plays VMI at home on Saturday. UNC Greensboro takes on Wofford on the road on Saturday.