Twenty-five homes were destroyed in Saturday`s strike in the densely populated Yarmouk district.
It came a day after a top army general threatened to step up attacks against the paramilitary Rapid Support Forces.
Fighting between the Sudanese army and the RSF broke out in mid-April as a result of a vicious power struggle within the country`s military leadership.
In early June, the RSF claimed full control of Yarmouk, an area of the capital which houses an arms manufacturing facility.
Later on Saturday, the warring factions agreed on a 72-hour ceasefire starting at 06:00 (04:00 GMT) on Sunday. It was announced by Saudi and US mediators. Similar ceasefires in the past have not been observed.
Precise figures on the number of people killed in the fighting are difficult to establish, but it is believed to be well over 1,000, including many civilians caught in the crossfire.
Roughly 2.2 million people have been displaced within the country and more than half a million are sheltering in neighboring countries, according to the UN.
Several ceasefires have been announced to allow people to escape the fighting but these have not been observed.
The recent attack targeted civilians in Mayo, Yarmouk, and Mandela areas, according to the RSF. The army has not commented.
Since the hostilities began, tens of thousands of civilians have fled across the border into neighboring Chad.
Doctors and hospitals there have been overstretched and struggling to cope.
The violence has also resurrected a two-decade-old conflict in Sudan`s western Darfur region.
