Friedl, 19, made his competitive debut in Bayern's 2-1 win at Anderlecht in the group stage of this season's UEFA Champions League on 22 November 2017. He took his Bundesliga bow in a 2-1 loss to Borussia Mönchengladbach three days later, but has not featured since.
"Even though Werder are fighting to stay in the league, they are a big club with great tradition," said Friedl. "Werder are well known in Austria thanks to players like Zlatko Junuzovic, Florian Kainz, Marko Arnautovic and Andreas Herzog. I'm happy to be part of this team for the next one and a half years."
"Marco is a young player who is capable of playing in central defence and at left-back," added sporting director Frank Baumann. "He's taken his first steps in professional football at FC Bayern and we now hope he can gain further experience and develop here. We're very pleased to have won the battle to sign him."
Friedl, who has also made 10 reserve-team appearances so far this season, joined the Bayern academy in 2008, at the same time as fellow countryman David Alaba - the club's first-choice left-back.
He has represented Austria at every youth level from the Under-15s up to the U-21s.