Alaba impressed at centre-back alongside Javi Martinez, Benjamin Pavard and Jerome Boateng in a string of Bundesliga victories before the mid-season break, and his performances fuelled speculation over a possible move to Chelsea.
But Flick, who has overseen five wins and two defeats in the league since being placed in temporary charge of the champions on November 3, said there were no plans to allow the versatile defender to leave the club.
"Alaba is doing very well at centre-back at the moment," Flick told reporters at the club's training camp in Doha.
"He's not for sale.
"He can lead a team, he showed that. He fulfills the criteria of a player who can marshall a defence."
Flick was reluctant to comment on the signing of goalkeeper Alexander Nubel from Schalke in a deal that will see the 23-year-old arrive in Munich at the end of the season.
Manuel Neuer has been ever-present in goal for Bayern this season and Flick said he is happy with Sven Ulreich in the role of deputy to the Germany international.
Nubel is seen as a potential long-term successor to Neuer, but Flick said: "I'm not interested in that now.
"Bayern took the chance to bring a talented goalkeeper to Munich. But Nubel will be a Bayern player in July.
"I'm satisfied with the current situation and Sven Ulreich is doing very well. Competition enables performances."