Crowell was the first rider through the final corner but was passed a few feet from the line by Sinead Miller (Marian College). Tammy Wildgoose (University of California-San Diego) finished third.
Crowell said she it was her strategy to lead out the sprint, unaware that Miller - a multi-time national collegiate and junior national track champion - was on her wheel.
"I'm obviously disappointed but I knew I had to go early," she said, "I did hear something today that made me feel a little better. Dave Towle (the race announcer) was saying you can't win if you don't risk losing. That's a good way to put it."
Crowell never ventured far from the front during the hour-long race along a 0.9-mile, figure-eight course. She also won a pair of point prime sprints, which helped her finish second in the omnium competition to Carla Swart (Lees-McRae College).
"I think I rode the best race I could today," she said. "Eventually, I'm going to win one of these times."
Friday, Crowell earned a bronze medal for her third place in the road race. She has one more chance to medal Sunday when she is part of Florida's four-rider squad in the 18-mile (28 km) team time trial.