Troutman entered the game with 976 career points and now needs only five more to reach 1,000.
The Phoenix led 39-29 at halftime, but Simpson's 3-pointer put the Spartans ahead 56-55 with 7:03 left and Nicholas Paulos made it 59-56 with 6:08 remaining.
Isenbarger's 3-pointer put Elon up 68-66 with 1:31 on the clock, and Troutman's and Beaumont's free throws clinched it.
Maryland point guard Melo Trimble, considered a lock to leave the program before struggling in the second half last season, has withdrawn from the NBA draft and will return for his junior season.
Louisville's Chinanu Onuaku, who recently underwent a medical procedure to correct a heart rhythm issue detected during the combine, will keep his name in the NBA draft pool.
Andrew White III will return to the Nebraska men's basketball team next season after removing his name from the NBA draft.