Flaherty's second TD was a 4-yard run on the second play of the fourth quarter, but the Redhawks quickly answered again with Nick Lee running one in from 2 yards with only 6:52 to play.
Beverly had an excellent opportunity to salt the game away with a strong final drive, which included a 5-yard run off an unbalanced quick pitch to Flaherty on a fourth-and-3 from Beverly's own 43-yard line. The Panthers fumbled the ball away on the goal line, however, to give Flutie and Natick one final chance with 1:19 to play.
Flutie advanced the Redhawks over midfield, but his final three passes fell incomplete.
"We wanted it real bad," Flaherty said. "I can't even explain how bad we wanted it, but I think it showed with our play."
Division 2A Super Bowl
Beverly 28, Natick 21
at Gillette Stadium, Foxborough
Natick (11-2) 7 0 7 7 — 21
Beverly (13-0) 0 14 7 7 — 28
N—Brian Dunlap 10 pass from Troy Flutie (Sam Lenson kick)
B—Kenny Pierce 27 run (Harry Brown kick)
B—Pierce 4 run (Brown kick)
B—Brendan Flaherty 3 run (Brown kick)
N—Dunlap 6 pass from Flutie (Lenson kick)
B—Flaherty 4 run (Brown kick)
N—Nick Lee 2 run (Lenson kick)
RUSHING: Natick — Troy Flutie 18-38, Nick Lee 9-37; Beverly — Brendan Flaherty 30-175, Isiah White 11-87, Kenny Pierce 7-71, Luke McDonald 1-11, Dave Rollins 2-3.
PASSING: Natick — Flutie 22-39-266-2-0; Beverly — Rollins 0-1-0-0-0.
RECEIVING: Natick — Alex Hilger 8-113, Andrew Boynton 7-64, Brian Dunlap 5-60, Justin Robinson 1-27, Nick Lee 1-2; Beverly — None.