Alec Peters scored 18 points, Darien Walker had 12 points and Vashil Fernandez chipped in eight points, 13 rebounds and three blocks for Valparaiso, which shot just 27 of 77 for 35.1 percent from the floor.
Peters had nine boards and Walker grabbed eight for the Crusaders, who outrebounded the Penguins 58-38.
Fernandez's dunk gave Valparaiso (14-3, 1-1 Horizon League) a 52-43 lead with 15:34 remaining. Youngstown State pulled within 61-58 with 8:13 left before Valparaiso closed on an 18-6 surge, with Walker hitting 7 of 8 from the line, to seal it.
Bobby Hain and DJ Cole scored 13 points apiece to lead Youngstown State (9-8, 0-2). Marcus Keene had 11 points and Osandai Vaughn 10 for the Penguins.