Matt Faulkner passed for 345 yards and the go-ahead touchdown for the Spartans (4-7), who ended a three-game losing streak. Ryan Otten also caught eight passes for 101 yards as Faulkner set career highs with 33 completions in 44 attempts.
Navy (4-7) lost its streak of eight straight years in a bowl game. Kriss Proctor rushed for 82 yards and a pair of touchdowns, and threw for 90 yards.
Navy scored on its first two possessions of the second half to take a 24-20 lead. Jon Teague kicked a 24-yard field goal midway through the third quarter and Proctor scored on a 2-yard run late in the period.
The go-ahead score was set up by a turnover. Jabaree Tuani tackled Faulkner, forcing a fumble. Jared Marks was right there to recover on the Spartans 43. Six plays later, the Midshipmen were in front.
Aaron Santiago's 21-yard run on a third-down play and Casey Bolena's 12-yard gain on a reverse were the key moments of the drive.
The Spartans responded just four seconds into the fourth quarter when Faulkner found freshman Jabari Carr for a 13-yard touchdown pass.
Rutley scored on runs of 3 and 1 yards.
Proctor was 9-of-20 passing, both second only to his 14-of-24 performance against Air Force.
The Midshipmen, who entered the game second in the nation in rushing offense, was limited to 254 yards on the ground, their third lowest total of the season.
San Jose State's Jens Alvernik connected on a pair of field goals to match the school's single-season record of 16.
Santiago also scored for Navy, which trailed 20-14 at the half.
Navy falls at San Jose State, 27-24
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