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.
Scott Van Pelt and Stanford Steve look back at "bad beats" from Week 13 in college football.
Michigan State quarterback Connor Cook joins Scott Van Pelt to discuss the Spartans' season and their chances of making the College Football Playoff.
USC named Clay Helton its permanent football coach on Monday, just days after he led the Trojans to the Pac-12 South championship.
SEC Network's Clint Stoerner and Matt Stinchcomb discuss how LSU football will move forward with Les Miles as head coach.
Florida head coach Jim McElwain gives his take on Alabama running back Derrick Henry during a press conference.
SEC Network's Maria Taylor, Dari Nowkhah, Matt Stinchcomb and Clint Stoerner discuss memorable moments from Week 13 of SEC football.