The slow return to normalcy came after an Ethiopian mediator announced that the protest leaders and the ruling military council had agreed to resume talks following a deadly crackdown on a weeks-long sit-in.
The negotiations collapsed last month because the two sides disagreed about whether a civilian or soldier should head a new governing body.
The launch of the civil disobedience campaign on Sunday came nearly a week after a raid on the sit-in outside the army headquarters in Khartoum on June 3 left dozens dead and hundreds wounded.
On Wednesday morning an AFP correspondent who toured parts of the capital saw buses waiting for passengers at their stations, while shops in some districts opened.
The main gold market in central Khartoum remained shut, and many residents still preferred to remain indoors given the heavy deployment of security forces across the capital.
"I'm still staying at my home because I'm worried about the presence of security forces carrying guns on the streets," said Samar Bashir, an employee in a private company.
Several other residents also told AFP that they were remaining indoors as internet services were still not fully restored across the capital, which made working from offices difficult.
Several private companies had also extended the Eid al-Fitr holidays up to the end of this week.
Sudan has been led by a military council since the generals toppled autocratic president Omar al-Bashir on April 11 after months of nationwide protests against his iron-fisted rule of three decades.
Following Bashir's removal, protesters camped outside the military headquarters in Khartoum for weeks to demand civilian rule until security and paramilitary forces dispersed them.