Virginia Tech won its final three games to finish 7-6.
"Not everything in life is real smooth," Hokies coach Frank Beamer said. "These players worked hard and how they reacted to adversity and to disappointment and when all of them wanted to do better they kept together."
Rutgers (9-4) had a chance to tie it in overtime, but Nick Borgese missed a 42-yard field-goal attempt to the right.
The loss ended a run of five straight bowl victories for the Scarlet Knights and kept them from recording their first double-digit win season since 2006.
The win also was the Hokies' 12th straight victory over their former Big East Conference rival.
Virginia Tech trailed 10-0 at the half, then rallied in the final 30 minutes thanks to some timely turnovers and offense. Quarterback Logan Thomas struggled in the first half and finished with a pair of interceptions, but also had 192 yards passing and the game's only passing touchdown.
"I can't commend the defense more," Thomas said. "The entire season that's kind of how it's been. I have to give a shout out to (linebacker) Bruce Taylor because he played his tail off the entire game. It felt like he was in the backfield making a tackle on every play."
Taylor finished the night with a team-high 11 tackles to lead a defense that held Rutgers to 67 yards in the second half.
Virginia Tech cornerback Antone Exum, selected the most valuable player of the game, picked off Gary Nova's pass early in the fourth quarter to set up the tying score.
He said though the offense took its lumps early, he was never down on their effort.
"That's just the way the game panned out," Exum said. "We never lose hope with the guys on the other side of the ball. Our job, honestly, is just to go out there and get as many three-and-outs as possible and give the most opportunities as we can to put points on the board.
"We did a good job of that tonight."
Rutgers seemed to be in command until the opening minutes of the fourth quarter, when turnovers and a sudden surge from the Hokies' offense quickly turned the momentum.
Down 10-0, Virginia Tech took over after Rutgers missed field goal and moved into Scarlet Knights' territory for the first time in the game on a 32-yard pass from Thomas to Dyrell Roberts.
Thomas then found Corey Fuller for a 25-yard strike on the next play, before the drive stalled on the 8. It forced the Hokies to settle for Journell's 25-yard field goal.
Exum intercepted Nova's pass on the ensuing drive, giving the Hokies a first down on the Rutgers 21.
The Hokies found the end zone three plays later on a 21-yard touchdown pass from Thomas to Fuller with 10:56 left as steady rain began to fall.
"We finally caught them off balance," Thomas said. "We finally got them uncomfortable. ... I just had to put the ball out there for him."
Virginia Tech defensive end Tyrel Wilson then came up with the defense's second turnover of the night, recovering a fumble inside the Scarlet Knights 40 after Nova dropped a snap while lined up in the shotgun.
An intentional grounding penalty on Thomas forced a punt, though, with less than 7 minutes to play.
They got another chance a few series later, only to see Journell's 51-yard field goal come up short with 2:20 showing on the clock.
Rutgers punted, but got it back just a play later when Thomas' pass was intercepted by Brandon Jones.
"Two tremendous defensive performances, and one of the better defensive performances I've seen from Rutgers players this season," Rutgers coach Kyle Flood said. "It's unfortunate that we came out on the wrong side of the game, and squander that kind of performance as a result."
It was defense on both sides that controlled the action in the first half as Rutgers took a 10-0 halftime lead.
The Scarlet Knights were the most effective offensively, managing a modest seven first downs and a field goal. But the Scarlet Knights came up empty on their best drive of the half, failing to convert on a fourth down pass play inside the Hokies 35.
Virginia Tech struggled throughout, though, tallying only 73 yards total in the first two quarters. Thomas was also sacked twice and intercepted late in the half, which severely hampered an offense that never made it into Rutgers' territory.
Penalties also bent in Rutgers' favor. Virginia Tech was penalized eight times for 60 yards. The Scarlet Knights weren't whistled for any penalties in the half.
A miscue by Virginia Tech on the opening drive of the game produced the game's first score.
Hokies center Caleb Farris sent his second snap of the night sailing past Thomas and into the end zone.
Thomas scrambled back to pick it up, and tried to run it out, but he was instantly swarmed and lost the ball as he was tackled. It was eventually recovered by Rutgers linebacker Khaseem Greene for the touchdown.
Beamer said the challenge to not any shortcomings from this season cloud the offseason.
"I couldn't be more proud of this team," he said. "We've won some more games in other years, but I think this group is special."
Notes: The game was the lowest scoring the bowl's history. It surpassed Stanford's 24-3 win over Penn State in 1993. ...The game also set a bowl record with 20 punts, passing the previous record of 19 in the 1991 matchup between Alabama and Colorado.
Follow Kyle Hightower on Twitter at http://www.twitter.com/khightower .
Virginia Tech 13, Rutgers 10
Rutgers 10 0 0 0 0 10
Virginia Tech 0 0 0 10 3 13
Rut • Greene recovered fumble in end zone (Borgese kick), 14:43.
Rut • FG Borgese 36, 2:38.
VT • FG Journell 25, 12:14.
VT • C.Fuller 21 pass from Thomas (Journell kick), 10:56.
VT • FG Journell 22.
Attendance • 48,127.
First downs 14 12
Rushes-yards 39-67 32-3
Passing 129 193
Comp-Att-Int 17-40-1 15-40-2
Return Yards 40 84
Punts-Avg. 10-36.3 11-42.2
Fumbles-Lost 2-1 5-1
Penalties-yards 4-35 14-95
Time of Possession 32:34 27:26
Rushing • Rutgers, Huggins 18-48, Shuler 1-25, Jamison 13-21, Team 1-(minus 1), Nova 6-(minus 26). Virginia Tech, Scales 12-14, M.Davis 1-11, Coleman 7-6, Gregory 1-2, Roberts 1-2, Holmes 1-(minus 2), Thomas 7-(minus 4), Team 2-(minus 26).
Passing • Rutgers, Nova 17-40-1-129. Virginia Tech, Thomas 15-39-2-193, Team 0-1-0-0.
Receiving • Rutgers, Coleman 4-55, Harrison 2-23, Jefferson 2-13, Pratt 2-13, Carrezola 2-6, Huggins 2-(minus 2), T.Wright 1-11, Shuler 1-9, Jamison 1-1. Virginia Tech, Coleman 5-39, M.Davis 4-62, C.Fuller 2-46, Roberts 1-32, Dunn 1-6, Phillips 1-5, Gregory 1-3.