The joint prayers were held at the Grand Basra Mosque on Monday.
In a speech after the prayers al-Sadr urged Iraqis to avoid civil discord and blamed the "US occupation" for the wave of sectarian attacks sparked by the bombing of the al-Askari shrine in the city of Samarra.
He also urged his followers to "resist the occupation by acts not by words".
On Saturday, the Association of Muslim Scholars (AMS)organised joint Sunni-Shia prayers in which Shaikh Abd al-Hadi al-Daraji, a top al-Sadr aide, participated.
The AMS has accused the US army in Iraq and regional powers of trying to spark a civil war in Iraq.
The association, which is regarded as Sunni Muslim, has refused to participate in the political process as long as foreign troops are present in Iraq.
Dr Muhamad Ayash al-Kubaisi, the AMS spokesman, told Aljazeera.net that stirring up a civil war in Iraq was a field tactic of the US forces in Iraq and strategic planning by some of Iraq's neighbours.
He said: "Engaging Iraqis in a bloody fight against each other will definitely distort the attention of Iraqi resistance fighters, and instead of fighting the Americans in Iraq they will be busy with the civil war."
"The shrines that were bombed in Samarra were not built recently, they have been there for 12 centuries, and their location is in a Sunni area; why they were hit now, why were there no such attacks before the occupation?"
Al-Kubaisi blamed the sectarian tension in some areas of Iraq on a regional power, although he refused to name which one.
"Engaging Iraqis in bloody fight against each other will definitely distort the attention of Iraqi resistance fighters, and instead of fighting the Americans in Iraq they will be busy with the civil war"
Dr Muhamad Ayash al-Kubaisi,
He said: "There are some regional powers whose interest is in dividing Iraq into smaller states that cannot stand for themselves, small tiny states that need protection."
Al-Daraji agreed with al-Kubaisi and blamed the US army in Iraq for much of the tension.
Shaikh Jawad al-Khalisi, a revered Shia scholar, sent a delegation to visit and help clean and reconstruct Sunni mosques that have been attacked after the Samarra blast.
Al-Khalisi told Aljazeera.net that "foreigners" would not succeed in breaking "our commitment to our religion and country".
The Shia delegation prayed at noon in a Sunni mosque in northern Baghdad, and continued working in the mosque before moving with a Sunni delegation for the evening prayer in a Shia mosque.