The news site reported that the recent stand-off has raised fears of a violent confrontation between protesters and the army.
Government buildings and private property were also attacked, spokesman Hashem Ali added.
Thousands of protestors were staging a sit-in for the sixth night running outside Khartoum army headquarters as the military council's curfew began at 10:00 pm (2000 GMT) despite growing global pressure to hand over to civilian rule. "We call on the masses to stay on the streets until all the demands are met".
On April 11, 2019, following months of protest nationwide, the First Vice President and Defense Minister of Sudan, Mr Ahmed Ibn Auf, announced the arrest of al-Bashir and his removal from power.
Lt-Gen Omar Zain al-Abidin, who heads the military council's political committee, said on Friday: "The solutions will be devised by those in protest".
The conflict in Darfur erupted in 2003 when ethnic black rebels took up arms against Khartoum's Arab dominated government, accusing it of neglecting the region economically and politically.
Ibn Ouf, who is under USA sanctions for supporting genocidal militias in the Darfur region, had been under global pressure to establish a civilian transitional government.
Who is in charge now?
Sudanese protesters rallied against the new military council in Khartoum on Thursday evening despite army warnings it would enforce a curfew. He is little known in public life. He has close ties to senior Gulf military officials as he was responsible for coordinating Sudan's military involvement in the war.
"All the 160 registered Malaysians in Sudan are accounted for and safe", the Foreign Ministry said in a statement today.
A military takeover has taken place in Sudan.
Bashir was overthrown on Thursday after weeks of mass protests brought on by rising food costs, high unemployment and increasing repression during his three decades in power.
Speaking at a news conference aired live on state TV and flanked by other uniformed officers, Zein Abedeen insisted the army has no ambition to hold the reins of power for long. "We will not dictate anything to the people".
The SPA said the military had announced a "coup" that would merely reproduce the same "faces and institutions that our great people revolted against".
Earlier on Saturday, the state-run media announced the resignation of Lieutenant General Salah Abdallah Gosh, who as the head of the National Intelligence and Security Services had overseen the crackdown against the protesters.
He said "no party will be excluded".
Meanwhile, Sudan's military council appealed on Friday for financial aid from regional peers to tackle a worsening economic crisis, a day after the ouster of president al-Bashir.
He promised people that the army will hand over to a democratic regime after a two-year transitional period.
Political parties and movements behind the protests said they were meeting Saturday with the military to discuss the transition, saying they've formed a 10-member delegation to introduce the people's demands to the military council.
Mr Bashir has also been indicted by the ICC on charges of war crimes and crimes against humanity in Darfur.
Asked whether the United States supported Bashir being put on trial before the International Criminal Court for Darfur atrocities, Palladino said: "We believe that the victims of Darfur deserve justice, that accountability is essential for achieving lasting peace in Darfur". He denies the allegations.
"The Sudanese people should determine who leads them and their future".
Analysts said Bashir's overthrow in a "palace coup" made the transition to democracy in Sudan a more distant prospect. The deposed leader is yet to be seen since Thursday's events.
Soon after the protests organised by the Sudanese Professionals Association began a week ago, a distressed Mr Bashir intimated to his inner circle that Mr Auf was his choice for a successor.