Renate Künast, 54, a parliamentary group leader of the resurgent Greens party, which is posting record support across the country and in the capital, said she would challenge Wowereit for city hall.
"I am ready – I am running for the office of Berlin mayor," the spiky-haired former party leader and ex-federal agriculture minister told a gathering of Greens members.
"Berliners want a new beginning and many of them want it with us."
Berlin is both the national capital and one of Germany's 16 federal states. The election is due in September 2011.
Künast, who is from the Greens' centrist camp, would be its first female mayor.
A popular Social Democrat (SPD), Wowereit coined the motto "poor but sexy" to describe the once-divided city, a slogan Künast slammed as a capitulation to 13-percent unemployment and a lack of industry.
Wowereit belongs to the party's left wing and has been mentioned as a potential rival to Chancellor Angela Merkel in 2013. But a defeat to Künast would likely dash those hopes.
The Berlin election is one of six state polls next year, which could also see Merkel's ailing conservatives punished.
A countrywide survey for ARD public television Friday showed the Greens at an all-time high with 22 percent support.
Merkel's Christian Union bloc tallied 32 percent, while their partners, the pro-business Free Democrats, were stuck at just five percent. The SPD posted 27 percent.
In Berlin, surveys show the Greens as the strongest party, with nearly 30 percent support.
Political scientists say the party is profiting from dissatisfaction with Merkel's fractious government as well as a re-invigorated anti-nuclear power movement.
Merkel's government controversially wants to extend the lifetime of Germany's 17 reactors by up to 14 years beyond a scheduled shutdown of around 2020.