The two were named as Khamis Abu Darwish and his brother Asri.
A large quantity of guns and grenades were found during house-to-house searches as well as a basement bomb factory.
The Information Minister is quoted as saying it had been decided that carrying any sort of weapons in Maan was now prohibited.
At least four people have been killed and 50 arrested - eight of them foreigners - since the government went into Maan in force at the weekend.
Officials have sought to portray the fugitives they are pursuing as arms smugglers, arsonists and killers.
They have denied the crackdown is aimed at Muslim militants.
However, some correspondents say the action is intended to send a message to opponents inside the kingdom that no trouble will be tolerated in the run-up to any American action against Iraq.
'Right-hand man'
Ecstatic police on the edge of Maan fired into the air after arresting the two men, the Associated Press news agency reported.
Khamis Abu Darwish is considered to the right-hand man of Mohammad al-Shalabi, also known as Abu Sayyaf - the key suspect being sought.
Shalabi and his associates are also accused of membership of a banned radical group, Takfir Wal-Hijra, the French news agency AFP said.
Jordan's Muslim Brotherhood movement offered to help mediate, but said on Wednesday the government had refused.
Information Minister Mohammad Adwan was quoted by AFP as saying Maan was now being declared a weapons-free area.
"This decision means that everyone must turn in their weapons to the security forces and that the security forces will search for weapons in every corner of Maan," he said.
Rocket-propelled grenades, machine-guns, ammunition, chemicals, explosives and military uniforms were said to have been found during searches in the city.
Maan has been under curfew since late Sunday, although it has been relaxed to allow people to shop for necessities and carry out other activities.
Witnesses said there was no sign of a withdrawal by regular troops backed by armour who reinforced counter-terrorism forces that went into Maan early on Sunday.
Anti-government sentiment
Senior officials have said the security sweep would end only when activists are jailed and illegal weapons seized.
Residents hid from gunfire on Tuesday, as security forces looking for militants and weapons conducted house-to-house searches.
The authorities are hunting down militant leader Mohammad Shalabi who escaped from Jordanian police custody last month.
The situation in Maan has been tense since Mr Shalabi was wounded in a shoot-out with police at the beginning of November.
The city has long been a troublespot. Islamist and anti-government sentiment is strong in the city and people retain close-knit tribal loyalties.
Mr Shalabi and others have been on the authorities' wanted list since riots in Maan at the beginning of the year, which followed the controversial killing of a student during his arrest by police.