Dr Besigye sought medical treatment after being tear-gassed in his car and bundled roughly into a truck when he was arrested on Thursday.
He later left Uganda for treatment in Kenya, and witnesses said he had to be supported as he boarded a plane.
It was Dr Besigye's fourth detention this month for his participation in a "walk-to-work" protest over high prices.
President Yoweri Museveni has said the walking campaign over the rise in the cost of living is illegal.
End Quote Brown Ndese protesterThey arrested him like a chicken thief - we cannot allow such things to continue”
Pepper spray After his arrest on Thursday Dr Besigye was charged with inciting violence but was released on medical grounds until 2 May.
The BBC's Joshua Mmali in the capital, Kampala, says Dr Besigye was taken to hospital from the court because he had been temporarily blinded.
On Friday evening, he was allowed by the authorities to fly to Kenya.
Our reporter says footage of the arrest was broadcast on Ugandan television and the video-sharing website YouTube.Continued