Flick was brought in on a temporal basis after Niko Kovac was dismissed in early November.
The 54-year-old has impressed the Bayern hierarchy in his short spell in charge, winning eight of his ten games so far.
Despite a difficult start to the season that has seen them lose four times already, Saturday’s 2-0 win over Wolfsburg took the Bavarians up to third on the Bundesliga table, four points adrift of leaders RB Leipzig going into the winter break.
Flick also led Bayern to three Champions League wins after taking over, making them the only side to win all six group stage games.
At a meeting between Flick, sporting director Hasan Salihamidzic and CEO Karl-Heinz Rummenigge on Sunday, it was decided that the interim manager’s spell should continue until the end of the season.
“We at FC Bayern are very satisfied with Hansi Flick’s work,” Rummenigge told the club’s official website.
“Under him as head coach, the on-field development has been outstanding, both in terms of the quality of our play and the results achieved.
“We set a new record in the 28-year history of the Champions League with six wins in six matches in the group stage, and in the Bundesliga we have returned to touching distance of the top of the table.
“I am convinced that FC Bayern will continue next year where we left off in the last few games, namely playing attractive and successful football.
“On behalf of FC Bayern as a whole, I wish Hansi Flick every success.”
Bayern Munich have been drawn against Chelsea in the round of 16 stage of the UEFA Champions League.
