Lynchburg (14-3, 5-3 ODAC) owned the glass, pulling down 54 of 89 missed shots, to win for the second time in eight lifetime meetings with SU (3-14, 0-8).
The LC Hornets outscored SU 38-16 in the paint and had a 23-6 advantage in second chance points.
The two teams traded the lead three times in the first 4:23 of the game before Alex Graves gave the visitors the lead for good on a layup at the 15:37 mark.
This bucket started a 20-7 run for LC and put the visitors in control for the remainder of the contest.
SU, on the strength of two fastbreak layups and a Jared Carithers 3-pointer, was able to cut the deficit to five points, 26-21, with 1:22 remaining in the first, but would get no closer.
After an SU Hornets run to start the second half make it 36-30 following a Sharif Almulla 3-pointer at 15:16, Lynchburg sealed the victory with a 10-0 spurt of the next 3:26.
LC led by at least 13 points the rest of the way.
Carithers and Almulla both had 16 points with Almulla also pulling down six rebounds.
Austin Chillemi had game-highs in points, 17, and rebounds, 13, for the victors.
Shenandoah is back in action on Wednesday at 7:00 at national power Virginia Wesleyan.