Josh Porter led the Pilots with 22 points, which included 5-of-9 three-point baskets from beyond the arc.
With the Pilots trailing by two and just over six minutes remaining in regulation, Porter hit two back-to-back NBA three's to put the Pilots back ahead by four.
The game would go back-and-forth over the next five minutes before Jamon Morris converted an old fashioned three-point play to give the Pilots a three point lead with 47 seconds remaining.
The Pilots defense then forced the Gold Rush to take a contested three-pointer that was just short; however, the Gold Rush grabbed the offensive rebound with 21 seconds left and had one last shot to tie.
A Mark Stewart three with four seconds left missed the whole goal, as J'Quincy Jones pulled down the Pilot rebound and was immediately fouled.
Jones made the first of two free throws with 3.6 seconds remaining, as the Pilots sealed the victory.
Travis Cash pumped in 18 points on 6-for-8 shooting from the field, while Jamon Morris also finished in double figures with 14 points.
Following a career-high 33-point performance in the semifinals, the Pilots held Xavier leading scorer Mark Stewart to just 5 points on 1-of-9 shooting from the three-point line.
Shaun Dumas led the Gold Rush with a game-high 23 points and seven assists, while Kelechi Okoroha added 18.
The Pilots will now await their seeding and opponent to be announced on Wednesday afternoon for the 2008 Buffalo Funds NAIA National Tournament.