The dismissal came as General Abdel Fattah al-Burhan's deputy in the ruling military council announced that the mastermind behind a deadly raid on a protest camp on June 3 had been identified.
Abdallah Ahmed will replace Al-Waleed Sayyed Ahmed as prosecutor general, the official SUNA news agency reported, without giving any reason for the sacking.
Bashir appeared Sunday in front of another prosecutor to face charges of corruption and illegal possession of foreign currency.
At least 128 people have been killed since the crackdown, the majority on the day the sit-in was cleared, according to doctors linked to the protest movement that led to Bashir's ouster.
The generals, who seized power after the army ousted Bashir on April 11 following a popular uprising, have so far resisted to transfer power to a civilian administration.
On Wednesday, Burhan called on protest leaders to resume talks without any conditions.
Protest leaders have expressed readiness to resume talks but on certain conditions, including an end to an internet blackout imposed after they launched a civil disobedience campaign earlier this month.
They are also seeking an international probe into the killings and the acceptance of all earlier agreements reached in previous negotiations with the generals prior to the crackdown.
Hundreds of protesters chanting "civilian rule, civilian rule," took part in demonstrations Thursday in several cities after organisers called for new rallies to pressure the generals.
Witnesses said rallies took place in Port Sudan, the country's main economic hub, in the central towns of Al-Obeid and Madani, and in the eastern town of Kassala.
"We came out today because our revolution is still incomplete. Our main demand is civilian rule and I'm sure we will achieve it," said Mohamed Khalil, a protester from Port Sudan.
Witnesses said dozens of employees from private companies and ministries, including oil and information, held silent demonstrations outside their offices in Khartoum.
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