Lieutenant General Abdel Fattah al-Burhan, the head of Sudan's sovereign council, said on Wednesday that the country's airpsace was open, and that all intelligence buildings were under the control of the army, following a revolt by former security agents linked to Sudan's toppled ruler Omar al-Bashir.
The violence was the biggest confrontation so far between the old guard and supporters of the new administration, which helped topple al-Bashir in April after 30 years in power.
The security agents surrendered late on Tuesday after negotiations with their leaders.
In a televised speech, al-Burhan said he would never allow a coup to take place.
Al Jazeera's Hiba Morgan, reporting from Khartoum, said: "After more than 15 hours of a standoff ... the Sudanese armed forces said the situation has been resolved.
"It looks like the situation, for now, has been contained."
Earlier, heavy gunfire erupted in Khartoum after the agents, who had belonged to a feared security service, rejected the financial compensation offered after their unit was disbanded.
Violence broke out at the Directorate of General Intelligence Service office, formerly known as the National Intelligence and Security Service (NISS) - the powerful security arm of al-Bashir.
Masked members of NISS dressed in military uniform set up checkpoints in one of Khartoum's main residential streets near the headquarters and were seen firing shots into the air, witnesses said.
In a televised statement, Information Minister Faisal Mohamed Saleh said the gunmen were former employees upset at the terms they had been offered upon their dismissal.
There were no immediate reports of casualties.
Authorities had closed Sudan's airspace for five hours as a precautionary measure after the start of the shooting.
The gunmen were angry after being told to either retire or join the notorious Rapid Support Forces (RSF) paramilitary group.
"The events that occurred today are under control," tweeted Prime Minister Abdallah Hamdok, a former World Bank economist. "We renew our confidence in the armed forces to contain the situation."
NISS security agents were at the forefront of cracking down on protesters during the nationwide uprising that erupted against al-Bashir in December 2018.
The army deposed al-Bashir four months later and the country's new authorities pledged to reform NISS - a key demand of the uprising that called for his removal from power.
'Create confusion'
Lieutenant-General Mohamed Hamdan Dagalo, deputy head of the military council and head of the RSF, said former Sudan intelligence chief Salah Gosh was behind the shootings.
"This is a coordinated plan by Salah Gosh and another member of the National Congress party including some generals from intelligence service," he told a news conference during a visit to Juba in South Sudan.
"The person behind this shooting today is Salah Gosh. He has many generals active within the security sector with an aim to create confusion and fighting."
Dagalo said while he would not consider Tuesday's incident a coup attempt, any such action would not be tolerated.
"We will not accept any coup, we will not accept any illegal change. The only change will come from the Sudanese people," he said.
Gosh could not be immediately reached for comment.
Authorities had closed Khartoum's airport because of the proximity to the site of unrest.