In his first Bundesliga match in interim charge of the first team, Flick watched his side dispatch Dortmund in clinical fashion at Allianz Arena on Sunday (AEDT).
Two goals from Robert Lewandowski, one from Serge Gnabry and an own goal from Mats Hummels made it two wins from two for Bayern this week after a 2-0 UEFA Champions League defeat of Olympiacos on Thursday (AEDT).
Bayern has been linked with Erik ten Hag, Massimiliano Allegri, Jose Mourinho and Arsene Wenger in its search for a full-time successor for Kovac, with Wenger stating on Friday that he expects to hold talks with chairman Rummenigge next week.
However, it seems Flick will stay in charge for the time being, with Rummenigge saying: "We will continue with Flick until further notice."
When asked if Flick would be in the role for the Bundesliga match at Fortuna Dusseldorf on 24 November (AEDT), Rummenigge replied: "You can expect that."
Rummenigge intends to speak with Wenger in the coming days to clarify the situation.
"I have respect for Arsene. We'll call him and clear things up. I don't want to have stress with him," he said.
Germany head coach Joachim Low, meanwhile, thinks his former assistant should be given the Bayern job permanently.
"I think so. He has the skill and a top emotional ability to deal with the players," he said.
"Hansi knows what to do. I think he can do it."
Bayern's win moved it to within a point of Bundesliga leader Borussia Monchengladbach, which faces Werder Bremen on Monday (AEDT).