Sudan's army has quelled a rebellion by former elite troops loyal to ousted leader Omar al-Bashir.
Shooting broke out on Tuesday in the capital Khartoum and the city's airport was briefly closed amid the clashes.
The violence was sparked by a row over severance pay for officers in a much-feared intelligence agency that is being overhauled.
Two soldiers were killed and four were injured in the worst unrest since Bashir was overthrown last April.
Officials say 40 of the mutineers surrendered and intelligence chief Abu Bakr Mustafa handed in his resignation after he was blamed for failing to collect weapons from the pro-Bashir forces.
Sudan has been jointly run by military generals and civilian leaders since August.
A senior member of the ruling Sovereign Council, Gen Mohammed Hamdan Dagalo, known as Hemeti, accused former intelligence chief Gen Salah Gosh of orchestrating the rebellion.
Gen Gosh's whereabouts are unclear, with speculation that he fled Sudan after Bashir was toppled.
Airspace now open
Gen Dagalo said that while he did not consider the violence a coup attempt, such action would not be tolerated.
And in a speech on Wednesday, the sovereign council head, Lt Gen Abdel Fattah al-Burhan, declared that the violence was now over.
"All headquarters are under the army's control, and the airspace is now open," he said.
Soldiers from the intelligence agency, the General Intelligence Service (GIS), posted videos of their colleagues firing heavy weapons into the night sky in a show of force.
Reuters news agency quoted residents as saying there was some fighting in a northern district of Khartoum and a security building had been seized by mutineers near the main international airport.
"This happened because those troops rejected the amount of money they got for their retirement," government spokesman Faisal Mohamed Saleh told state television.
The country's main protest group had earlier called for an end to "these irresponsible operations that are causing terror among citizens".
At least 170 people were killed during the months-long crackdown against the protest movement last year.
The GIS, then known as the National Intelligence and Security Service (NISS), played a major part in the crackdown.
It was Sudan's most-powerful security agency during Bashir's 30-year rule and protesters had demanded its disbandment as a key part of the transition to democracy.
The former president, who was eventually overthrown by the military following the protests, was sentenced to two years in a social reform facility for corruption in December.