Troutman hit 8 of 11 shots and Bonney, who played 21 minutes, made 7 of 10 for the Phoenix (10-7, 3-2), who never trailed and led 42-27 at the half.
Elon began the second half with a 9-0 run, which included two layups by Troutman, to make it 51-27, and the Phoenix maintained a lead of at least 17 points until the final 1:29.
Bobby Austin, who scored 19 points to pace the Paladins (4-12, 1-4), scored seven points in the final 2:05, including a 3-pointer at the buzzer. Colin Reddick had 18 points for Furman, which lost on the road for the 11th straight time, including eight this season.
Ryley Beaumont finished with 10 points and nine rebounds for Elon.