Evan Mawarire, who launched the #ThisFlag protest campaign on social media, was found not guilty by High Court judge Priscilla Chigumba after state prosecutors failed to prove their case.
The ruling came as Zimbabweans wait to see whether new President Emmerson Mnangagwa, a former deputy of Mugabe, follows through on pledges of democracy after years of violations of basic freedoms.
There are still some Zimbabweans "in prison for political reasons, in terms of having stood up against the regime" of Mugabe, Mawarire said outside the courthouse in downtown Harare, the capital.
"Many are still appearing in court over the next few weeks and I want to urge this new government and administration to drop those charges and let those people go, because they did not commit any crime at all."
Mawarire, who stood in the dock with a Zimbabwean flag, said he was "absolutely elated" at his acquittal, but said it was too soon to tell whether it reflected a trend toward more independence in the judiciary, which was often subject to political pressure during the Mugabe era.
"It could be evidence of a freer Zimbabwe, but I think also this case had no legs from the beginning," Mawarire said.
"I think that a lot more needs to be seen for us to determine whether this is a free judiciary going forward."
Prosecutors sought to link Mawarire to stone-throwing and other violence during protests last year that were the largest Zimbabwe had seen in a decade.
They cited videos posted on social media in which the pastor urged people not to go to work and shop owners to close their businesses as a way of expressing opposition to the government.
They said the pastor must have foreseen that his calls could lead to violence. In her ruling, the judge acknowledged that Mawarire was trying to "cripple government operations," but said he urged "passive resistance" and exercised his constitutional rights to freedom of assembly and expression.
"There is no evidence that he urged a violent removal of the government," she said. Instead, Mawarire "preached peace and repeatedly told his audience not to resort to violence."
The 93-year-old Mugabe resigned on Nov. 21 after the military moved in and the ruling party turned against him.
His final days in power also saw large demonstrations by a population troubled by years of economic decline and mismanagement under Mugabe, whose aura as an independence leader after the end of white minority rule in 1980 eroded over the decades.