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.
Sources: Baltimore Ravens targeting Michigan Wolverines' Mike Macdonald to be new DC
The Ravens have targeted Michigan defensive coordinator Mike Macdonald, a former Ravens assistant, to be John Harbaugh's next defensive coordinator, sources told ESPN.
Lawyers claim LSU fired athletics official Sharon Lewis, who sued department, in retaliation
Lawyers for an associate athletic director who filed a $50 million federal racketeering lawsuit against Louisiana State University say she has been fired in retaliation and asked the court Wednesday to add that claim to her suit.
Oklahoma State All-Big 12 CB Jarrick Bernard-Converse transfers to LSU
Jarrick Bernard-Converse, a first-team All-Big 12 cornerback at Oklahoma State, has transferred to LSU.
Sources: Oklahoma State set to hire Derek Mason as defensive coordinator
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San Diego State Aztecs add QB Braxton Burmeister as transfer
Quarterback Braxton Burmeister, who started at Virginia Tech last season, is transferring to San Diego State.
Michigan Wolverines AD Warde Manuel added to College Football Playoff selection committee
Michigan athletic director Warde Manuel is one of four new members added to the College Football Playoff's 13-member selection committee, which will be chaired by NC State AD Boo Corrigan.