Flynn, making only his second career start behind center as Most Valuable Player-candidate Aaron Rodgers took the week off, flung his sixth scoring strike of the day with 1:10 remaining, finding to Jermichael Finley for the go-ahead score.
Flynn outdueled Detroit's Matthew Stafford in the regular season-ending shootout, which saw the top-seeded Packers overcome cold, snowy conditions to finish their season at 15-1.
Stafford ended with 520 yards and racked up five touchdowns for the playoff-bound Lions (10-6).
But he also sealed Detroit's loss by tossing an interception to Sam Shields in the final minute.
The game marked the first time in NFL history two quarterbacks threw for at least five touchdowns and 400 yards apiece in a single contest.