Flores hit BJ Fleming down the left sideline for a 76-yard touchdown with three minutes to play for the winning points after giving up a 35-7 lead.
Eastern Washington responded with Kekoa Visperas' fourth TD pass, third to Efton Chism III with a minute left but the Lumberjacks recovered on the onside kick.
Flores scored on runs of 1, 1 and 6 yards in the second quarter to put the Lumberjacks (5-6, 5-3 Big Sky Conference) on top 35-7. Chase Belcher and Devon Starling had scoring runs of 9 and 30 yards, respectively, in the first quarter.
A 35-yard scoop-and-score by Jaren Banks and Chism's 39-yard TD reception cut it 35-21 at the hall. Then Tuna Altahir scored on a 62-yard run and Chism's 13-yard reception tied the game at 35-all early in the fourth quarter.
But NAU marched 75 yards to regain the lead on a 14-yard pass from Flores to Marcus Phillips Jr., and after an EWU punt Fleming put it away.
Flores was 14-of-20 passing for 262 yards and ran for 114 as the Lumberjacks piled up 581 yards. Starling ran for 125.
Visperas was 24 of 40 for 284 with Chism catching eight for 103 yards. The Eagles (4-7, 3-5) finished with 430 total yards.
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