The decision had been taken after 52 people were killed in the southern Iraqi city of Karbala in fighting between the Mahdi Army and another Shia bloc - the Supreme Iraqi Islamic Council (SIIC), whose armed wing controls much of the south.
On Thursday, Iraqi security forces arrested 72 fighters following the Karbala clashes, the defence ministry said.
A ministry statement said a number of weapons had also been confiscated during a search of homes across the southern city.
Test of authority
Analysts said al-Sadr's six-month order would be a test of his authority over the group, which is believed to have fragmented and, according to the US, has received funding, training and weapons from Iran.
Also on Wednesday, Nuri al-Maliki, the Iraqi prime minister, said that fighters from the Mahdi Army and the SIIC who were involved in the violence in Karbala had wanted to blow up the Imam Hussein shrine, one of the holiest to Shia Muslims.
"From our initial investigation, we found some evidence of who did this act ... the intention of this act was to storm into the shrine of Imam Hussein and blow it up," al-Maliki said from inside the shrine during a visit to Kerbala, 110km south of Baghdad.
The Mahdi Army denied the allegation.
While his ministers have left the cabinet, al-Sadr's political bloc holds 30 seats in parliament and is still part of the ruling Shia alliance.