Alaa, 53, and Gamal, 51, were released from Tohrah prison early this morning, an official source from the Ministry of Interior told state media.
Their release comes a day after the violent anniversary of the 2011 uprising that toppled Mubarak.
Last week, an Egyptian court ordered Ala and Gamal's release from detention in a graft case pending retrial after the court accepted their appeal.
Mubarak and his sons are charged with acquiring almost 126 million pounds from the presidential palace budget and using the money for the construction and development of family-owned assets.
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In May last year, Mubarak was sentenced to three years in a maximum security prison on embezzlement charges. His sons were also sentenced to four years in prison.
Collectively, they were fined 125 million pound and are required to repay 21 million pound.
Last November, an Egyptian court cleared Mubarak and seven former security commanders, including his former interior minister Habib al-Adly, against charges of killing anti-government protesters during the 2011 revolution.
Mubarak, 86, was retried on charges of complicity in the killing of unarmed protesters during the 2011 revolution that ended his 30-year rule.