LSU (3-2) had won 49 consecutive home games against non-conference opponents, but Troy (4-1) dominated from start to finish, forcing three turnovers and converting two of those into touchdowns.
The Trojans converted 10 of 18 third downs and both fourth-down plays while holding LSU to 0 of 8 on third down.
Troy raced to a 17-0 lead when Chunn scored from the 1 on the Trojans' first possession of the second half.
LSU freshman Myles Brennan replaced Danny Etling at quarterback in the third quarter and threw a 7-yard touchdown pass to Foster Moreau to cut the deficit to 17-7, but Brennan's interception on LSU's next possession led to Troy's 10-play, 64-yard drive for a 24-7 lead. Josh Anderson got the payoff with a 7-yard run.
Etling returned midway through the fourth quarter and threw a 34-yard scoring pass to Russell Gage, making it 24-14 with 7:41 left. Etling added a 20-yard scoring pass to Moreau with 1:59 left to pull LSU within 24-21, but Troy recovered the onside kick and punted with 20 seconds left.
This was Troy's third meeting with LSU. In the first two meetings, Troy lost close games -- 24-20 in 2004 and 40-31 in 2008. The 2008 loss was particularly tough because the Trojans blew a 21-point lead in the second half.
Troy normally speeds up the game by running a quick-tempo offense, but the Trojans slowed things down and kept LSU's defense on its heels in the first half, converting 7 of 11 third down to take a 10-0 lead.
Troy also converted a fourth-and-9 from the LSU 41 just before halftime that turned into a 37-yard field goal by Evan Legassey as time expired.
With seven seconds left in the second quarter and no timeouts, Silvers threw a crossing pattern to wide receiver John Johnson, who was tackled at the LSU 20 as the clock appeared to have run out.
Upon reviewing the play, however, the officials ruled Johnson was tackled with two seconds left -- the clock should have stopped for the first down -- and they called both teams back onto the field from their locker rooms.
The Trojans snapped the ball on the referee's signal, and Legassey's 37-yard boot hit the crossbar and fell over for the 10-0 lead.
Troy forced a big turnover on the first play of the game. Nick Brossette was slammed by Cedarius Rookard and the Trojans recovered at the Tigers' 30. Five plays later, Silvers kept on a read option and scored from the 1 for a 7-0 lead.
LSU, meanwhile, was doing nothing on offense. The Tigers' biggest threat came in the second quarter, when Etling drove them to a first-and-5 at the Troy 19. But Etling threw long in the end zone for Stephen Sullivan on third down and Jack Gonsoulin duck-hooked a 35-yard field goal attempt.
LSU failed to convert on all three third-down attempts and also was unsuccessful on a fourth-and-1 at the Troy 33 in the first half.
NOTES: Sitting in a motorized chair, House Majority Whip Rep. Steve Scalise, who was gunned down while practicing for a Congressional charity baseball game in July, greeted LSU coach Ed Orgeron on the sideline before kickoff. Scalise, an LSU graduate, returned to work Thursday on Capitol Hill and was given a standing ovation in the House of Representatives. He was joined on the sideline by wife Jennifer and their two children, Maddy and Harrison. ... RB Nick Brossette's fumble on LSU's first play from scrimmage was the first Tigerd fumble in 315 consecutive carries.