Soon after the couple - Maryam Nawaz and Muhammad Safdar - arrived from London on Monday morning, Safdar was taken into custody by an NAB team.
The court also issued perpetual warrants for the arrest of Nawaz Sharif's two sons, and separated their trial from other members of the family.
Some senior PML-N officials, including Maryam, have hinted that elements of Pakistan's powerful military had a hidden hand in the Supreme Court disqualification that forced Nawaz to resign.
Safdar told Geo News that the couple had chose to return to Pakistan on the advice of their lawyers.
Hussain and Hassan left for London to be with their mother, Kulsoom, who is battling throat cancer.
Sharif attended the previous two hearings but went to London last week to see his ailing wife.
Sharif's lawyer Khawaja Harris asked the court to adjourn hearing for 15 days with commitment that Sharif would also appear.
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On Monday, the accountability court declared Hassan and Hussain proclaimed offenders for repeatedly failing to appear before it.
Television footage showed some supporters from the ruling Pakistan Muslim League-Nawaz (PML-N) trying to stop the vehicle from leaving the airport, including some who lay down in front of it. Nawaz Sharif, Maryam Nawaz and Captain Safdar will likely face indictment on the next hearing whether Sharif is present or not in court.
The judge barred Safdar from leaving Pakistan without its permission but rejected the NAB's request to confiscate his passport.
Meanwhile talking to media, Maryam Nawaz said despite serious reservations, they were appearing before the Courts in respect of the rule of law.
Sharif, his children - Hussain, Hassan, and Maryam, and her husband Captain Safdar are expected to appear in court on October 9 and be indicted in the corruption cases.
She described the charges against the Sharif family as "false allegations with no answers". Maryam and Safdar were granted bail yesterday in the Panama Papers case.