Middle Tennessee (3-3, 1-1 Conference USA) also got a touchdown from Brad Anderson, who scored with a 29-yard throw from John Urzua and finished with a career-high 112 yards rushing on 11 carries.
Florida International (3-2, 2-1) tied the game in the first quarter with a field goal by Jose Borregales but Middle Tennessee took over from there. Anderson put the Blue Raiders on top for good with the TD catch and then Thomas punched in his first two TDs, both up the middle.
Alex McGough, who finished 20-of-31 passing for 209 yards for FIU, cut the gap to 24-10 midway through the third quarter with a 13-yard TD run, and later connected with Thomas Owens on 4-yard touchdown pass but the Golden Panthers never got closer than 10 the rest of the way. Owens finished with 162 yards with 11 catches.
ThomasŐ third touchdown came midway through the fourth quarter on a sweep to the right from the 4 and he finished with 20 yards rushing. His longest carry was just eight yards.