Kizza Besigye's eyes were damaged by pepper spray when he was arrested in April
He was arrested four times and accused of inciting violence during the protests, in which Ugandans were urged to walk to work.
On one occasion, he was beaten by police, sparking further protests.
Human rights groups condemned the suppression of the protests, in which at least nine people died.
Mr Besigye was defeated in February's presidential election but says it was rigged.
The government accused Mr Besigye of trying to organise an
Egypt-style uprising and seeking to gain power through the streets after
losing the election.
Magistrate George Wetyekere acquitted Mr Besigye of the three
remaining charges - disobeying lawful orders, rioting after
proclamation and incitement of violence.
Another charge of inciting violence had already been dropped.
The magistrate also stressed that the public had the right to hold public demonstrations.
Mr Besigye sought medical treatment in Kenya after he was assaulted and sprayed with pepper spray in his car in April.
He says the charges were political.
Before the previous elections in 2006, he was charged with both treason and rape - and was later acquitted on both counts.
He was previously President Yoweri Museveni's personal doctor, but the pair fell out.
Mr Besigye left the country, saying his life was in danger, but returned in 2005 with the introduction of multi-party politics.
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