Hillman scored touchdowns on runs of 20, 2 and 2 yards before setting up his game-winning score with an 18-yard run with less than two minutes left.
San Diego State (8-4), which is likely to get a bowl bid, overcame a 21-point deficit.
Fresno State (4-9) built a 21-0 lead halfway through the second quarter after Isaiah Green scored on a 59-yard return of a blocked field goal, and Derek Carr's two touchdown passes.
But the Aztecs cut the lead to 21-14 at halftime before the second of Hillman's three short touchdown runs gave the Aztecs a 28-21 lead late in the third quarter. Robbie Rouse's 2-yard run tied the score in the fourth quarter.