Ekbote was arrested soon after the Supreme Court turned down his anticipatory bail plea earlier in the day, the official added.
"We arrested Ekbote from his residence here and he will be produced before the court tomorrow," a senior Crime Branch official said.
Last month, while extending the right-wing leader's protection from arrest, the apex court had asked the Pune rural police to submit a detailed report on the case and allowed them to question Ekbote.
Following directions from the court, Ekbote had appeared before the Shikrapur police for questioning for five times.
Today, the police submitted a detailed report in the apex court and sought the "custodial interrogation" of Ekbote, while opposing his bail plea.
Before submitting the report in the Supreme Court, a senior police officer had said, "In order to investigate the case properly, his custodial interrogation is required."
A case was registered against Ekbote and Sambhaji Bhide for allegedly inciting the anti-Dalit violence that left a man dead near the Bhima Koregaon war memorial in the district on January 1 during an event to commemorate the bicentenary of the Bhima-Koregaon battle.
Subsequent protests had disrupted normal life in Mumbai and other parts of Maharashtra.