Demonstrators who have been holding almost daily anti-Bashir protests rejected the decision to set up a transitional military council to run the country for two years and vowed to continue protests until a civilian government is established.
Activists are said to have called for mass Friday prayers outside the defense ministry compound, a focal point for protests.
Activists wearing yellow vests controlled traffic around the compound on Friday morning and managed foot traffic to and from the sit-in.
They also blocked a major bridge in central Khartoum.
Bashir (75) had faced 16 weeks of demonstrations against him. Announcing the president’s overthrow, Defence Minister Awad Mohamed Ahmed Ibn Auf said elections would be held at the end of the two-year interim period.
World powers, including the United States and Britain, said they supported a peaceful and democratic transition sooner than two years.
Speaking on state television on Thursday, Ibn Auf said Bashir was being detained in a “safe place” and a military council, which he is heading, would now run the country.
Sudanese sources told Reuters that Bashir was at the presidential residence under “heavy guard”.
Ibn Auf also announced a state of emergency, a nationwide ceasefire and the suspension of the constitution.
State television said there would be a curfew from 10 pm to 4 am.
Ibn Auf was due to meet journalists later this Friday.
The main organiser of protests against Bashir, the Sudanese Professionals Association, rejected Ibn Auf’s plans.
It called on protesters to maintain their sit-in outside the defense ministry.
In a challenge to the military council, thousands of protesters remained in front of the defense ministry compound, and in other parts of the capital, as the curfew went into effect.
They chanted “They removed a thief and brought a thief!” and “Revolution! Revolution!”
Reports say some shops in Omdurman, across the River Nile from central Khartoum, remained open past 10 pm.
Bashir has been indicted by the International Criminal Court in The Hague and is facing an arrest warrant over allegations of genocide in Sudan’s Darfur region during an insurgency that began in 2003 and led to the death of an estimated 300 000 people.
He denies the allegations.
Bashir’s downfall was the second time this month that a leader in the region has been forced out after mass demonstrations. Algeria’s Abdelaziz Bouteflika, in power since 1999, stepped down on April 2 after six weeks of protests.