Tension had further soared between the two sides after a brutal raid on a longstanding protest camp outside army headquarters in the capital Khartoum that killed dozens of demonstrators and wounded hundreds on June 3.
Dubbed the "Justice First" marches, Saturday's demonstrations were called by the Sudanese Professionals' Association (SPA), which has been spearheading the protests since December that led to the military ousting of longtime leader Omar al-Bashir in April.
The political transition deal is meant to end the impasse between the military council and the protest movement since security forces razed a massive pro-democracy sit-in in Khartoum early last month, killing more than 100 people, according to protest organizers.
Bashir was ousted by the army on April 11 after thousands of protesters camped outside the military headquarters in central Khartoum from April 6. Authorities, however, put the death toll at 61, including three security force members. African Union envoy Mohammed el-Hassan Labat originally said a meeting would take place Saturday night. "The military council should be held accountable (for) the massacre", said protester Samer Hussein.
Protesters were seen waving Sudanese flags and posters that read: "Freedom, Peace and Justice" and "Civilian (authority) is the people's choice".
Hundreds rallied and waved Sudanese flags in Omdurman - Khartoum's twin city - while crowds also marched through the streets of Port Sudan, the country's main economic hub, witnesses said.
At least 11 people were killed in clashes with security forces, according the organisers.
The announcement of the failed coup attempt came at a time when legal advisers to the military and protesters leaders were discussing the details of the agreement between the two sides at a hotel in Khartoum.
It was expected the final details of the power-sharing agreement would be announced on Thursday, but it's unclear whether that will now happen.
The military and a pro-democracy coalition agreed last Friday on a joint sovereign council that will rule for a little over three years while elections are organized.
They also agreed to delay the establishment of a legislative council until the sovereignty council and the civilian government are established.
A military leader is to head the council for the first 21 months, followed by a civilian leader for the next 18.
Dagalo is also the commander of the feared paramilitary Rapid Support Forces which protesters and rights groups allege carried out the June 3 raid.