The Bears entered Thursday's doubleheader with a 1-0 series lead in a best-of-three finale but fell short in both attempts for the championship, losing 12-6 and 11-9 in Portsmouth.
The opener saw Shawnee State trailing 10-1 after four innings with Mount Vernon racking up 15 hits in the game.
The Bears rallied in the seventh and eighth, but the surge was no match for the sizable lead.
Third baseman Nick Ball went 4-for-5 for the Bears with an RBI in game one while teammates Kyle Hammondtree, a senior, and Philip Butler were both 2-for-4.
Starter Cory Pallutch was handed the loss for his four innings on the mound while Cougar hurler Caleb Wright went 8.2 innings and gave up four earned runs in the win.
Mount Vernon's Jordan Doherty went 3-for-6 with six RBIs and a home run while Matt Parks was 3-for-4 including a homer for the Cougars.
In game two Shawnee State came out firing when senior Brian Ramey, a Green High School graduate, rocketed a three-run home run over the massive center field wall for an early advantage.
Camden Sauls and Rickey Masson scored along with Ramey on the three-run dinger.
The gained momentum was short lived however as Mount Vernon answered with a three-run home run of its own. Steve Williams drove his two-out round-tripper to right field and evened the score at three.
Over the next three innings an unfortunate trend developed as Shawnee State went cold at the plate and Mount Vernon kept up the long-ball marathon.
In the second, third and fourth innings the Cougars hit two-run home runs to mount a 9-3 lead. Doherty air-mailed two of the three homers and Ian Durbin had the third-inning RBIs.
A three-run sixth inning from the Bears cut the MVNU lead in half and included back-to-back solo home runs from Ramey and Zach Byler.
Starting pitcher Adam Wamsley, of Wheelersburg, had an up-and-down bottom of the sixth to continue the Shawnee State hot streak. Then in the seventh, Byler sent another one over the center field fence to put the Bears within two.
Mount Vernon again countered with a run on three hits and an error in the bottom of seven and a lead-off home run by Chaz Gibson in the eighth (the Cougars fifth homer of the game).
A two-run ninth by Shawnee State on three hits and an error put the final tally at 11-9 as the Bears, the AMC regular season champions, missed out on the NAIA National Tournament by a pair of runs and end the 2010 season with a 30-29 record.
The 2010 season weas the last for SSU in the AMC. The Bears join the Mid-South Conference next year.