The road victory gave Baker its fifth straight win and they improved to 7-1 on the year and 5-1 in the HAAC, while the Vikings fell to 5-2 overall and 5-1 in the conference.
Clark also nailed a 59-yard field goal with 11:26 to go in the game to tie the game up at 10-10.
The Wildcats led for most of the contest, as they scored first in the first quarter on a two-yard touchdown run by senior Dillon Baxter. Baker shutout MVC in the first half and enter halftime up, 7-0.
Then Lucas Guilfoil finally put the Vikings on the board in the third quarter with a 35-yard field goal.
Malachi Daniels than added a six-yard touchdown run in the fourth quarter to put MVC up, 10-7.
But the freshman kicker/wide receiver took over from there and knocked in two field goals to give Baker its first win over Missouri Valley since 2008. Baker head coach Mike Grossner is now 4-6 all-time against the Vikings.
The Baker defense held the Vikings to just 90 yards rushing and 2.8 yards per carry and sacked MVC quarterback twice, both coming from Adam Novak.
The Wildcats also forced three turnovers with an interception in overtime by senior Emmerson Clarke and Mike Stevenson along with Jared Fromm each forced a Viking fumble.
Offensively the Wildcats struggled a bit against the No. 1 rated defense in the country, as Baxter ran for 70 yards and Jake Morse was 9-of-20 for 89 yards and a pick.
Baker will return home next Saturday, Nov. 2 to take on Evangel University on the annual 'Black Out' game. Fans are asked to wear black to the game and 'Blackout' Liston Stadium.