They declared a general strike, joining unions in sectors such as healthcare and aviation, although they said they would continue to supply flour, cooking gas and emergency medical care.
The main market, banks and fuel filling stations in Khartoum were still closed on Thursday. Hospitals were providing only emergency services. Smaller shops were open, but there were long queues for bread.
In a sign of continued Western support for the ousted civilian cabinet, U.S. Secretary of State Antony Blinken tweeted overnight that he had spoken by phone to Foreign Minister Mariam Sadiq al-Mahdi.
Blinken said he condemned the arrest of civilian leaders in Sudan and discussed with Mahdi "how the U.S. can best support the Sudanese people’s call for a return to civilian-led transition to democracy".
A source close to ousted Prime Minister Abdalla Hamdok said he remains committed to a civilian democratic transition and the goals of the revolt that toppled long-serving autocrat Omar al-Bashir two years ago. Hamdok, initially held at Burhan's residence, was allowed to return home under guard on Tuesday.
In a statement, a group of members of the ousted cabinet rejected the coup and called on government employees to join protests and civil disobedience to bring it down. They also called for the release of Hamdok and their colleagues.
Several people have been killed in clashes with security forces since the takeover, and opponents fear the army-led authorities could deploy more force.
The source close to Hamdok said the prime minister had called for the military to avoid violence against protesters.
Opponents of the coup have been handing out fliers calling for a "march of millions" on Saturday against military rule, falling back on old methods of mobilisation with the authorities restricting the use of internet and phones.
The protest is being called under the slogan "Leave!" used in the protests that brought down Bashir. Since the anti-Bashir uprising, protests have been organised through neighbourhood committees that can mobilise locally without access to the internet or to major roads closed by security forces.
Sudan has been in the midst of a deep economic crisis with record inflation and shortages of basic goods, which only recently showed signs of possible improvement helped by aid that major Western donors say will end unless the coup is reversed.
More than half the population is living in poverty and child malnutrition stands at 38%, according to the United Nations. The healthcare system is in a state of collapse.
The military takeover brought an end to a shaky transitional set-up intended to lead Sudan to elections in 2023 by sharing power between civilians and the military following Bashir's fall.
Burhan's move reasserted the army's dominant role in Sudan since independence in 1956, after weeks of mounting tension between the military and civilians in the transitional government over issues including whether to hand Bashir and others over to the Hague where they are wanted for war crimes.
Burhan has said he acted to stop the country slipping into civil war and has promised elections in July 2023.
With backing from the United States, the transitional government had won Western debt relief, secured Sudan's removal from a U.S. list of states that sponsor terrorism, and taken steps to normalise ties with Israel.
The United States has frozen $700 million in aid for Sudan since Monday's takeover, and on Wednesday the World Bank said it was halting disbursements for operations in the country.
The Friends of Sudan -- governments which have supported the transition -- condemned the takeover in a statement issued late on Wednesday.
But while signatories included Britain, the United States, France and Germany, there were notable omissions, including Saudi Arabia and the United Arab Emirates, rich Gulf Arab states with whom Burhan has developed ties.
(Reporting by Khalid Abdelaziz in Khartoum and Nafisa Eltahir in Cairo Writing by Tom Perry Editing by Peter Graff) ((firstname.lastname@example.org; Reuters Messaging: email@example.com))