Mohammed Musabah al-Waili on Saturday said he was suspending Major General Hassan Sawadi and was also demanding the resignation of General Abdul Latif Thaban, the commander of the Iraqi army's Basra-based 10th Brigade.
Waili said the two security chiefs were suspected of links to "sabotage groups, from outside the city and abroad, that are carrying out sabotage and terrorist attacks".
The governor also accused two prominent Shia clerics of sharing the blame for a recent upsurge in violence in the city.
"I put the legal responsibility on Sheikhs Mohammed Falak al-Maliki and Sayed Imad al-Batad for provoking the people to stand up against the law and create chaos," Waili said in a statement released by his office.
The two men are representatives in the province of Shia spiritual leader Grand Ayatollah Ali al-Sistani. Waili called on the religious hierachy to rein them in.
"I demand their religious leadership to direct them back into the mainstream of the nation," he said.
Basra, which is mainly Shia, is close to the Iranian border and has seen an increase in violence since a helicopter crash last week in which five British service personnel died.
British forces in Basra have been isolated since the regional government broke off all contact in February. Local authorities finally lifted the ban last week but the situation remains tense.