Temple (3-2) has won three straight games to run its unbeaten Mid-American Conference record to 3-0. The Cardinals fell to 0-6 (0-2 MAC).
Pierce added a third game to a record he set last week, when he became the first freshman in school history to rush for 100 yards in two straight games.
The Owls led 10-0 after a 27-yard field goal from Brandon McManus and a 28-yard touchdown pass from Vaughn Charlton to James Nixon. Ball State's.
Dan Ifft caught a two-yard pass as time expired, for Ball State's final score.