Flynn shot 10-of-23 from the field and scored 9 of Syracuse's last 10 points in regulation.
And he was able to break free off an inbounds play in the waning second of regulation to set up the Rick Jackson free throw that sent the game to overtime.
"He's a talented, talented player," said Marquette head coach Buzz Williams. "When it was time to get one, he was the one to get one."
The Orange, who put the game away by finishing overtime on a 9-2 run, led for all but 2:09 of the second half, and it was thanks to some late-game heroics by Jerel McNeal that Marquette was able to come back enough to force the extra session.
McNeal, the senior playing in his final home game for Marquette, used his defense to help engineer a 10-0 run that gave Marquette a 70-67 lead with 3:01 to play. Then, with Marquette down 72-70 in the final minute, he hit a three with 17.9 seconds left in regulation to give his team a one-point lead.
"He's a big-time player," said Marquette's Wes Matthews. "He took a broken play into his own hands and shot with confidence."
McNeal scored 18 of his game-high 25 points in the second half and in overtime.
"He's the most confident player I've ever been around," said Matthews. "Combine that with toughness, heart, and talent and anything can happen."
After McNeal hit another big three-pointer to tie the game at 77 with 2:49 remaining in overtime, Andy Rautins answered with a three of his own to put the Orange up for good.
Rautins scored 20 off the bench for Syracuse, including 4-of-9 from three-point range. Jackson also came off the bench to record 17 points and 5 blocks for the Orange.
Syracuse's only lead of the first half came on a Jackson dunk off a slick volleyball-style redirect from Rautins with 2:57 left in the first half. The Orange trailed 35-34 at the half and took the lead back a minute into the second half.
"One-through-seven, they're as good as any team we've played all season," said Williams.
Marquette received a tremendous effort off the bench from Jimmy Butler, who collected 12 points and 14 rebounds to record his first career double-double. Butler also had 4 assists and no turnovers.
"Jimmy played the best game of his career," said Matthews. "He wanted it more."
Matthews also finished with a double double – notching 14 points and 12 rebounds – and Lazar Hayward added 17 points.
The Golden Eagles outrebounded the Orange 42-38, and their 23 offensive boards helped them record a season-high 33 second-chance points.
Syracuse, however, controlled the transition game, outscoring MU 22-10 on the break. In their previous three games, one-third of Marquette's points allowed were transition points.
The Golden Eagles now hold the No. 5 seed in the Big East Tournament and will play either St. John's or Georgetown Tuesday at 1 PM CST at Madison Square Garden.