Werner, who arrived from Werder Bremen before the beginning of last season, leaves after 351 days at the helm having guided Leipzig to a third-place finish in the Bundesliga and successfully overseeing a squad rebuild following a series of major player departures. His assistants Tom Cichon and Patrick Kohlmann have also been relieved of their duties.
The decision marks yet another managerial change at the Saxony club, with Werner the third permanent head coach in just 14 months.
Leipzig's sporting director Marcel Schafer confirmed the decision followed an internal end-of-season review.
"We have spent the past few days carrying out a thorough final review of the recent season," Schafer said. "On Tuesday evening, we decided that a change of head coach was needed.
"They played a major role in our successful rebuild and in qualifying for the Champions League. Nevertheless, we believe the challenges ahead require new ideas and a different approach."
He added: "We thank Ole, Tom and Patrick for their work and dedication to RB Leipzig and wish them all the best for the future, both personally and professionally."
Behind the scenes, reports in Germany suggest the decision had been in motion for several weeks, with the club's leadership group - including Oliver Mintzlaff, Jurgen Klopp and Mario Gomez - said to have been aligned on the need for a new direction.
Werner had previously been tasked with stabilising a squad that narrowly missed European football the season before, and he ultimately delivered Champions League qualification. However, Leipzig are understood to be seeking a stylistic shift ahead of the new campaign.
Attention now turns to his successor, with Argentine coach Martín Demichelis emerging as the leading candidate after a brief spell at Mallorca, where he was unable to prevent relegation from La Liga's top flight.
Leipzig will begin pre-season preparations on 13 July, with their first competitive fixture of the 2026/27 campaign set to come in the DFB-Pokal first round against Eintracht Trier between 21–24 August. Their 11th consecutive Bundesliga season begins a week later, with fixtures released on 2 July.
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