The field goal was Manton's third in a tight game that saw four lead changes - two in the final quarter.
The Warhawks (3-1, 2-0) had jumped out 13-0 but were behind 20-19 midway in the fourth quarter after Brandon Silvers put Troy (0-5, 0-1) up 20-19 with his third TD pass, a 6-yarder to Chandler Worthy.
Silvers passed for 270 yards but scrambled four times to nurse along a 98-yard drive before halftime, tying the longest scoring drive in Troy's D-I history.
Louisiana-Monroe's Pete Thomas passed for 328 yards with two TDs, both to Ajalen Holley - a season-long 64-yarder early and then a 15-yarder to take a 19-14 lead in the third.
Louisiana-Monroe extended its best-in-the-nation active streak of forced turnovers to 30 games.