Jones had 117 yards rushing on 16 carries for the Panthers (3-3, 1-2 Conference USA). James Morgan threw for 160 yards and two touchdowns.
FIU scored four consecutive touchdowns in the first half, staring with Morgan's scoring pass to Shemar Thornton late in the first quarter for a 7-3 lead. Charlotte answered with a touchdown to take a 10-7 edge. The Panthers continued the streak with Kaylan Wiggins' 4-yard touchdown run early in the second quarter to put them back on top, 14-10. Napoleon Maxwell ran into the end zone from 13 yards out to cap the next FIU drive, and Morgan hit Jones for a 5-yard TD pass to close the half with a 28-17 advantage.
Jones opened the second half with three consecutive touchdown runs, from 5, 41 and 13 yards, to push the Panthers' lead to 48-23 with 9:58 to play.
Benny LeMay ran for 144 yards and a touchdown for the 49ers (2-4, 0-2).