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.
If San Diego State receives a bowl bid, it will mark consecutive bowl appearances for the first time in its 43 years at the Division I level.
The Aztecs, who recorded consecutive winning seasons for the first time in 15 years, gained 496 yards in offense as they came back from the early Fresno State lead.
Carr completed 19 of 35 passes for 336 yards and had touchdown passes of 88 yards to Jalen Saunders and a 23-yarder to Josh Harper. But the Bulldogs were held to just one touchdown in the final 40 minutes.
San Diego State's Ryan Lindley was 21 of 40 for 281 yards and finished the regular season as San Diego State's career leader in passing yards, passing touchdowns, total offense and completions.
Cody Wichmann blocked Abel Perez's 51-yard field goal late in the first quarter and Green converted it into a 7-0 lead. Fresno State's blocked field goal was the ninth time it has blocked either a field goal or extra-point attempt this season. The Bulldogs lead the NCAA in blocked kicks since 2002.
On its next possession, San Diego State drove to the Bulldogs' 1, but Hillman was stopped short of the end zone on fourth down.
Four plays later, Carr threw a long pass that Saunders caught for the 88-yard touchdown. Carr added a 27-yard TD pass to Josh Harper for a 21-0 lead with 9:14 left in the second quarter.
The Associated Press contributed to this report.