Their wish was fulfilled on 11 April, when the military terminated al-Bashir’s three-decade rule and placed him under house arrest.
But the move wasn't enough for the protestors, who refuse to see an army dominated by al-Bashir’s appointees in control of the country’s fate for fear that they might cling to power as did their predecessor.
Amid these concerns, thousands of demonstrators refuse to leave the streets, keeping up a sit-in outside the military headquarters in Khartoum set up on 6 April.
Demonstrators have called for an "immediate and unconditional" transfer of power to a four-year civilian government, while the military has said its own transitional council will rule for up to two years until elections can be organised.
"They said they want to stay for two years, we will stay three years," said Abubakr al-Awad, 23, who warned that Sudanese people will suffer under their rule.
Alongside the sit-in defiance, protesters are waving national flags, chanting "freedom" and banging plastic drums in the sweltering summer heat, while others man makeshift clinics or prepare meals for other demonstrators.
The Sudanese Professionals Association, which spearheaded the protests, has called on people to join the sit-in and defend it from any attempts by the military to disband it and disperse the demonstrators, regardless of the relentless sun, with temperatures hovering above 40 degrees Celsius (100 Fahrenheit).
Nearby the sit-in, doctors and nurses staffing clinics are set up and a network of volunteers helps keep the demonstration going.
"There is a system in place where those who have, give, and those who don't have, take," said al-Awad, a recent medical school graduate.
The new graduate has been volunteering since last week, spending most of his time helping patients from the sit-in.
On Tuesday, loads of demonstrators suffered from heat exhaustion, and in one clinic a man could be seen receiving an IV drip.
Meanwhile, adjacent to the clinics, a group of women prepare lunch in tents for the protesters, while volunteers contribute their money to purchase supplies to make food for those who need it.
"We don't want people to go back home," Razan Hassan al-Tayeb, 29, said.
"People come just as they are and they don't come with anything, so we are trying to make people not go back home hungry or thirsty or something like that," said al-Tayeb, who was helping prepare a meal of lentils.
He comes from a five-person family but says they are struggling with life even though four of them are working.
"Outside the sit-in, it's a different place but inside the sit-in, this is the place that we dream of — freedom, where you can speak and have a voice. You can say whatever you want. Whatever you desire to say and reach the people," she said.
Since the toppling of Omar al-Bashir on 11 April, the country's junta has been shaken by radical and swift changes, sometimes with noteworthy concessions to protesters' demands.
Lieutenant General Awad Ibn Auf took the oath to become the head of the council on 12 April, but only to resign one day after amid mass protests calling for a civilian-led transitional administration.
The general was replaced by Lieutenant General Abdel Fattah al-Burhan, who announced a bundle of concessions in effort to appease protesters calling for a civilian-led transition.
He vowed on Saturday to "uproot [al-Bashir's] regime", giving in to protesters’ demands to see remnants of the ancient regime eradicated.
As demonstrators keep up their sit-in outside the army complex, reports circulating on Wednesday said military rulers have transferred the ousted al-Bashir, whose whereabouts had not been known, to Kobar prison in Khartoum.
Nearby witnesses said there was a heavy deployment of soldiers and members of a paramilitary group outside the prison.