The civil disobedience campaign had brought the Sudanese capital to a standstill.
Its decision reflected a growing desire for the protest leaders and the ruling military council to avoid a further escalation, after a week of violence.
A protest strike kept businesses shut and residents indoors in the Sudanese capital Tuesday as a top USA diplomat prepared a visit to press the ruling generals to halt a bloody crackdown.
On 7 June, Ethiopian Prime Minister Abiy Ahmed flew to Khartoum in an attempt to reach a political solution.
Cyber security monitor Netblocks said "an nearly total blackout" started around noon local time.
They didn't stop until al-Bashir was forced out by his military generals in April, ending three decades of autocratic rule.
Sudanese opposition leaders have since called for the army to allow a civilian-led interim body to govern the country.
Special envoy Mahmoud Dirir told reporters in Khartoum that the military also agreed to release political prisoners as a confidence-building measure.
The UN Security Council on Tuesday urged all sides "to continue working together towards a consensual solution to the current crisis" and voiced support for African-led diplomatic efforts.
Before the meetings, the State Department said Nagy was going to urge the parties to work toward an environment conducive to the resumption of negotiations.
The state-run SUNA news agency said Sudanese diplomat Elham Ibrahim had met with Nagy soon after his arrival.
Rasha Awad, editor of the Sudanese daily Al-Tahgyeer, said the FDFC had gambled on global pressure after last week's violent crackdown.
The protest movement itself said in a statement that it was calling on people "to resume work from Wednesday".
After three days of virtual paralysis in the capital, an Ethiopian mediation representative announced that both sides had agreed to return to the negotiating table.
Rights groups continued to express alarm over the situation.
Amnesty and Human Rights Watch warned United Nations peacekeepers Tuesday against withdrawing from Sudan at a time when the Janjaweed militia is not only keeping up war crimes in Darfur but also taking its "despicable brutality" to Khartoum.
The council condemned the recent violence in Sudan and called for an immediate halt to attacks against civilians, stressing the importance of upholding human rights.
Internet monitoring platform NetBlocks is reporting a "near total restriction" on Sudan's remaining internet connectivity as of 12:00 p.m. UTC Monday 10 June, amid reports of deadly attacks perpetrated by Sudanese paramilitary groups. For months, pro-democracy activists had demonstrated, demanding al-Bashir's ouster, but they wanted him replaced by a civilian government - not a military junta which includes people who were loyal for years to the autocrat.