Austin Peay (2-1) has now won two straight under first-year coach Mark Hudspeth.
Each team kicked two first-half field goals and the game was deadlocked at intermission, 13-13.
JaVaughn Craig, who finished 18 of 32 for 252 yards, opened the second with a five-yard strike to Baniko Henry to put the Governors on top for good, 20-13 and Jackson pushed to 27-13 with his first pick six, this one from 29 yards out.
Robert Riddle got the Bears within a touchdown with a 4-yard pass to Chris Ellington to cut the Mercer (2-1) deficit to 27-20, but Austin Peay opened the fourth quarter with a touchdown run by Williams from three-yards out and a 69-yard pick six by Jackson that pushed the lead to 41-20.
Mercer's Riddle finished 29 of 47 for 287 yards and four touchdowns, but his two interceptions resulted in 14 Austin Peay points.
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