Sudan's security and intelligence chief, Salah Gosh, resigned on Saturday, state media reported.
"The chief of the transitional military council, Abdel Fattah al-Burhan, has accepted the resignation of... the chief of NISS," the council said.
Protesters in Sudan said on Saturday they would keep up pressure for civilian rule after the defense minister stepped down abruptly as transitional leader following the overthrow of President Omar al-Bashir.
Defense Minister Awad Ibn Auf stepped down as head of the transitional military council late on Friday after only a day in the post, as protesters demanded faster political change.
Celebrations erupted on the streets of Khartoum, where thousands of jubilant protesters waved flags and illuminated mobile phones in the darkness and drivers hooted car horns. People chanted: "The second has fallen!" a reference to Ibn Auf and Bashir, witnesses said.
The Sudanese Professionals Association (SPA), which has been leading the protests, called for more demonstrations on Saturday.
"Today, we continue the march to finish the victory for our victorious revolution," the SPA said in a statement.
"We assert that our revolution is continuing and will not retreat or deviate from its path until we achieve ... our people's legitimate demands of handing over power to a civilian government," it said.
The new head of the military council, Lieutenant General al-Burhan, is a commander believed to be more ready to talk to demonstrators.
Burhan was the third most senior general in the Sudanese armed forces.
"What happened is a step in the right direction and is a bow to the will of the masses, and we have come closer to victory," said Rashid Saeed, an SPA spokesman, adding the group planned more protests on Saturday.
Burhan said on Saturday a civilian government would be formed after consultations with the opposition and promised the transition period would last for a maximum of two years, as protesters kept up pressure for rapid change.
In his first televised address, he said he was also cancelling a night curfew ordered by his predecessor and ordered the release of all prisoners jailed under emergency laws put in place by Bashir.
Bashir, 75, who seized power in 1989, had faced 16 weeks of demonstrations.
Burhan was one of the generals who reached out to protesters at the week-long encampment near the military headquarters, meeting with them face to face, and listening to their views.
A Sudanese police spokesman said in a statement on Saturday that at least 16 people were killed, and 20 injured by stray bullets at protests and sit-ins on Thursday and Friday.
Government buildings and private property were also attacked, spokesman Hashem Ali added.