San Diego (6-1, 4-0 Pioneer League) went ahead 24-17 on Mills' 3-yard pass to Brandon White with 9:09 left in the game before Hoekstra's punt return at the 7:42 mark.
Drake (5-2, 3-1) got close on Trey Morse's 2-yard touchdown run with 3:48 remaining, but after the kickoff the Toreros ran out all but the final 34 seconds.
Mills completed 26 of 36 passes for 306 yards and hit Sam Scudellari for TD passes of 2 and 6 yards.
Drake's Mike Piatkowski was 21 of 37 for 296 yards and threw an 18-yard touchdown pass to Joey Orlando midway through the third quarter. The Bulldogs tied the score at 17 on Jacob Schmudlach's 2-yard run less than four minutes into the fourth quarter.