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.
https://www.bbc.co.uk/news/world-africa-51112518
I wouldn't say it was troops loyal to Bashir, BBC got it wrong here. It was factions of the security forces who were loyal to Bashirs regime doing the shooting.