The Owls (6-2) won their sixth straight game, their longest streak since 1974. The last time Temple went to a bowl game was the 1979 Garden State Bowl.
The Owls led 14-10 at halftime after Pierce's 68-yard run and Nixon's school-record 100-yard return.
Pierce, a freshman, carried the ball 29 times and became the first Temple player since Paul Palmer in 1986 to rush for more than 200 yards in consecutive games.
Navy (6-3) had a five-game winning streak snapped and, because it plays a 13-game schedule, still must win again to become bowl eligible. The Mids last won six in a row in 1979.
Last week, Pierce gained 212 yards in a 40-24 win over Toledo. Pierce has gained 1,033 yards this season and is the first Temple back to gain 1,000 yards rushing since 2002. He has rushed for 100 yards in five of his last six games.
Nixon's kickoff return came at a crucial time for the Owls as Navy had taken a 10-7 on a 3-yard punt return by David Wright when Owls punter Jeff Wathne bobbled a snap and punted quickly from his own end zone. The kick reached the 10 and Wright picked the ball up at the 3 after it bounced off a teammate.
Temple was the first team this season to hold Navy without a defensive touchdown in the first half.
The 274 yards rushing by the Owls were the most against Navy since Notre Dame rushed for 280 yards in 2003.
All three of Navy's touchdowns came following a Temple miscue, the shanked punt, a fumble and an interception.
Navy rushed for 227 yards with Vince Murray getting 115 yards on 33 carries, the third straight game he's topped 100 yards.
Kriss Proctor had 52 yards rushing and 31 yards passing, but was intercepted in the end zone on a badly underthrown pass.