Shenandoah (21-7) led 6-2 after scoring two runs in the eighth, but saw H-SC (9-18) bring the tying run to the plate with two outs in the ninth.
Freshman Matt Riegler, who came on in relief of junior Nick McMahon (5-0) midway through the eighth, induced a potential game-winning groundball, but the play was booted for a double error allowing Hampden-Sydney to cut the deficit in half.
Riegler then got a fly to left to end the game and collect his fourth save of the spring.
McMahon kept his record perfect after allowing two runs on nine hits and three walks in 7 1/3 innings of work. He also struck out four.
Riegler got out of the eighth on a strikeout and a comebacker before giving up a single and walking two in the ninth.
Senior Cory Nelson led the Hornets offense with a 2 for 3 day that included two RBI and two runs scored.
In the second, Nelson scored the first SU run of the game by doubling down the leftfield line and coming home on a Michael Paul single to right center.
Nelson had a sacrifice fly in the before doubling to right center in the eighth to plate Corbin Lucas with what proved to be the game-winning run.
Paul brought Nelson home with the final run of the contest one batter later on a single up the middle.
Billy Nixon (0-1) took the loss, allowing four runs on six hits in 4 1/3.
Shenandoah hosts No. 3 Christopher Newport for a two-game set beginning Friday night at 6.
Notes: The win makes the 2012 senior class the winningest class in school history. The 11 seniors have won 134 games to date since coming to SU in the fall of 2008... Coach Kevin Anderson now has 399 career wins...