Khalil Marzook, assistant secretary general of Wefaq, was accused of "inciting terrorism" and supporting a youth movement blamed for many attacks.
Mr Marzook was arrested in September after giving a speech at a rally.
He was released on bail the following month, after the opposition boycotted national dialogue talks in protest at his detention and the lack of progress.
The government formally suspended the dialogue in January and it has not since reconvened.
However, earlier this month the information minister said meetings between government and opposition representatives were continuing.
‘Rare good news’
Mr Marzook was acquitted on Wednesday following a brief hearing. As he left the court building, he told journalists that he expected a travel ban put in place after he was charged to be lifted.
"My innocence was inevitable from day one," he said. "The political process has to develop and become effective for us to lead Bahrain to the shores of safety through negotiations and a comprehensive process that serves the interests of all the citizens of Bahrain."
The prosecution had accused Mr Marzook of exploiting his position at Wefaq to "call for crimes that are considered terrorist acts under the law".
It alleged that in his speech to a rally in the village of Saar on 6 September, he had openly supported the February 14 Coalition, a youth protest movement that the authorities have designated a terrorist organisation and blamed for a series of bombings and other attacks.
However, Human Rights Watch said it had seen a video of the speech and that Mr Marzook had not promoted violence at any point. It quoted him as saying: "We can only support a movement as long as it is peaceful. We transparently declare: the dividing line for us is violence."
However, at the end of the speech, a masked man handed Mr Marzook a flag that appeared to bear the emblem of the coalition, which he then held for 45 seconds, Human Rights Watch said.
Mr Marzook is a former deputy speaker of parliament who resigned along with other Wefaq MPs when the government launched a deadly crackdown on pro-democracy demonstrations in February 2011.
The protesters were demanding more rights and an end to discrimination against the majority Shia community by the Sunni royal family.
Brian Dooley, the director of the US-based campaign group Human Rights First, welcomed Mr Marzook’s acquittal as a "rare piece of good news from Bahrain".
"Marzook needs to be out of jail to be part of a negotiated settlement to Bahrain’s crisis. But so do other political leaders still in prison. If real dialogue is ever to begin it will have to include opposition figures beyond Wefaq," he said in a statement.
