The Falcons (6-3, 4-1 Mid-American Conference) won their fifth straight. They've allowed just 33 points and three touchdowns in those five games and haven't given up a touchdown in their last two.
Eastern Michigan (1-7, 0-4), which had gained 1,201 yards in its past two games, was held to 178 by the Falcons, who limited Massachusetts to 118 yards in a 24-0 win last week.
Jones punctuated the effort with a 23-yard touchdown return after Martin sacked Eastern Michigan's Tyler Benz.
John Pettigrew carried 24 times for 136 yards for the Falcons, who became bowl-eligible.