Early Hannibal turnovers and a pair of big plays for Jefferson City had the Jays ahead late in the first half.
But turnovers began to add up for the Jays and the Pirates powered their way to a game-sealing score as Jefferson City fell 32-21 on Friday night at Adkins Stadium.
Down 25-21 to begin the fourth quarter, the Jays forced a three-and-out to set themselves up 51 yards from the end zone.
Jefferson City quickly moved the chains as Seth Brooks completed an 11-yard pass to Marshaun Dye and ran it for a first down on third-and-2.
After Daylon Reading wrapped up Brooks for a loss of a yard on first down, Brooks tried to squeeze a pass to tight end Will Berendzen, resulting in an interception for Drake Dudley. It was Hannibal's third pick of the game.
"I think maybe a little bit of it's me trying to get greedy," Jefferson City coach Scott Bailey said. "I've got some really good skill players and I'm trying to get them the ball, so we're forcing some things."
The Pirates then wore down the Jays with its rushing attack, draining about 6 minutes off the clock with an 11-play, 55-yard drive that ended with Damien French scoring from two yards out.
French ran it 15 times for 69 yards and two scores.
Hannibal didn't gain more than eight yards on any run play that drive, but converted a pair of short third downs and averaged 4.1 yards per rush.
"Probably defense getting tired," Bailey said. "It's the same when we were able to get our run game going later in the second half. It takes more energy to react to a play than it does to create the play, so that's why defenses kind of tire as the game goes along."
Hannibal opened the game with a four-play scoring drive that ended with receiver Aneyas Williams taking a toss for a 22-yard touchdown run after quarterback Courtland Watson faked a handoff to French.
The Jays converted a turnover into a score late in the first quarter.
Fred Wilson recovered a fumble at the Hannibal 8-yard line and David Bethune scored from a yard out. Bassil Ahmed tied it at 7 with the extra point with 2:55 left in the quarter.
French scored from three yards out with just :17.9 left on the first-quarter clock to put Hannibal back in front.
But Jefferson City again turned defense into offense to take the lead.
Defensive end Frank Gillmore rushed into the backfield to take down receiver Kaiser Greenwell for an 8-yard loss to turn the Pirates over on downs.
Then on fourth-and-inches, Bethune got around the right side of the defensive front seven and sprinted to the end zone for a 43-yard score. Ahmed's extra point made it 14-13 with 8:21 left in the first half.
Bethune ran it 15 times for 49 yards and two touchdowns, while Brooks gained 49 yards on 17 rushing attempts.
"Our run game got going a little better tonight," Bailey said. "And for us to be successful going through the rest of the year, it's going to have to become more consistent inside and outside."
After a fumble recovery for Ethan Garnett, Brooks sailed a long pass into the hands of Dye along the home sideline for a 34-yard touchdown on a third-and-14. Ahmed's extra point extended the lead to 21-13 with 3:43 on the clock.
Hannibal pulled within 21-19 on a 20-yard touchdown pass from Watson to Joey Worthington late in the half and the Pirates turned an interception into the go-ahead score in the third quarter.
Watson completed 11-of-14 passes for 228 yards.
Watson concluded a 10-play drive by walking into the end zone from a yard out for a 25-21 lead at the 4:52 mark of the third quarter.
Jefferson City (0-2) will travel to Columbia next Friday night to take on the Rock Bridge Bruins for the first Central Missouri Activities Conference game for the Jays.
Rock Bridge (2-0) is 1-0 in the conference after Friday's 42-0 win at Sedalia Smith-Cotton.