The Seahawks scored the first eight points and led until a 7-0 run, punctuated by a dunk by Dan Garvin, put Bryant up 47-43 with 6:40 left.
But Wagner responded by scoring 22 of the final 28 points, including 9 of 11 free throws, to seal it.
The teams both failed to shoot even 35 percent from the field, but Wagner outrebounded Bryant 45-36, including 17-10 on the offensive glass and the Bulldogs made just 14 of 24 (58.3 percent) free throws. The Seahawks made 15 of 20 from the foul line.
Gavin led Bryant (5-11, 2-1) with 14 points. Curtis Oakley - the nephew of former NBA-star Charles Oakley - scored 12.