The Transitional Military Council (TMC) had suspended the talks late on Wednesday after two outbreaks of violence around protest sites in the capital Khartoum.
Street protests and a sit-in outside the Defense Ministry have continued since the army ousted and arrested former President Omar al-Bashir on April 11.
Demonstrators are calling for a rapid transition to civilian rule, and demanding justice over the deaths of dozens of people killed since protests triggered by an economic crisis and decades of repressive rule spread across Sudan from Dec. 19.
The TMC and the Declaration of Freedom and Change Forces (DFCF) have agreed on a three-year transition before elections, but have been deadlocked over whether civilians or the military would control a sovereign council that would hold ultimate power.
The Sudanese Professionals Association (SPA), which spearheaded protests against Bashir and heads the DFCF, has accused the TMC of dragging its feet in the talks and has sought to increase pressure on the council by expanding protests.
It also held the TMC responsible for street violence over the past week in which several protesters were killed and dozens wounded.
The council accused protesters of not respecting an understanding on de-escalation while talks were under way.