Zach Coleman hit a 3-pointer that gave the Blackbirds a 54-53 lead with eight minutes to go and they never again trailed.
After JoJo Cooper missed the second of two free throws, Wagner's Nigel Jackson grabbed the offensive rebound and was fouled with 13.7 seconds left. He hit both foul shots to make it 67-all before Batts' winner.
Romone Saunders led Wagner (11-6, 4-2) with 18 points, Cooper added 15 and Blake Francis scored 11.
The Seahawks missed half of their 20 free-throw attempts.