The court of the cassation ordered a retrial of the head of the Al-Wefaq political formation before the appeals court, said a judicial source.
The same court overturned three death sentences and seven life imprisonment sentences against a group convicted of killing three police, including an Emirati officer in a bomb attack more than two years ago.
Salman had been sentenced in July 2015 to four years in jail after being convicted of inciting hatred in the Sunni-ruled Gulf kingdom.
But the appeals court in May more than doubled his jail term to nine years after reversing an earlier acquittal on charges of calling for regime change by force.
Salman's arrest in December 2014 sparked protests in Shiite-majority Bahrain.
The cassation court had rejected a request to release the cleric earlier this month.
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His jail sentence came during a crackdown on the Gulf nation's largest opposition group, which has been dissolved by a court order over accusations of "harbouring terrorism".
Al-Wefaq had the largest bloc in parliament before lawmakers walked out in February 2011 in protest over a deadly crackdown on Arab Spring-inspired protests.
The crackdown on Wefaq has drawn criticism from UN chief Ban Ki-moon and Bahrain's allies in Washington, as well as rights groups.
Hundreds of Shiites have been arrested and put on trial since security forces backed by Saudi-led troops crushed in March 2011 month-long protests that demanded democratic reforms.
Authorities have also stripped at least 261 people of their citizenship since 2012, according to the Bahrain Centre for Human Rights, including the country's Shiite spiritual leader Sheikh Isa Qassim.
In the other ruling, the court of cassation ordered a retrial of the case of 10 defendants found guilty of planting a bomb in March 2014 in Deih Shiite village, which killed an Emirati police officer and two Bahraini policemen.
The Emirati officer was part of the Saudi-led Gulf force.
Appeals court had on May 31 upheld the three death sentences and life terms for the other seven who were also stripped of their citizenships.