The 23-year-old forward has scored 50 goals in 93 league appearances for Leipzig, who secured a return to the Champions League by finishing third.
Rangnick, who will return to his position as sporting director with Julian Nagelsmann taking over as head coach from 2019-20, stated Leipzig have still not received an approach for Werner, despite him being available for the right price.
"I would not be so sure that [Werner] will actually go to Bayern," Rangnick told Sport Bild.
"If Bayern were absolutely sure about Timo, they would have already officially contacted us with a request. Anything else would be unusual for Bayern, especially since we have a good relationship with them.
"Our position has not changed: we do not want him to go into the last year of his contract without an extension.
"He can leave this summer when a club comes who is willing to pay a suitable transfer fee."
Leipzig have a chance to win the DFB-Pokal for the first time in their history when they face Bayern in the final in Berlin on Saturday.
The club's CEO, Oliver Mintzlaff, admitted last week he is still hopeful Werner could extend his deal after the final.
Leipzig enjoyed a better season in the Bundesliga than 2017-18 – when they finished 6th – but were still comfortably beaten to the title by Bayern.
Ragnick's side came third, 12 points back from the eventual champions, although Borussia Dortmund pushed the Bavarians close and finished runners-up by just two points.
Saturday's final will mark the last game in a farewell season for wingers Franck Ribery and Arjen Robben.
The duo are both set to depart this summer after dominant spells at Bayern, and Werner could be one possible recruit to replace their attacking threat.