The businesses targeted were the Seoudi supermarket chain and Zad department store, respectively owned by Abdel Rahman Seoudi and Khairat al-Shater -- both leaders of the blacklisted Brotherhood.
"Security forces are implementing the law," Cairo's police chief, Brigadier General Ali al-Demerdash, said in relation to the moves.
"A committee formed in accordance with a court ruling decided to seize Zad, which is owned by Khairat al-Shater, and Seoudi, which is owned by Abdel Rahman Seoudi, because the two leaders are financing the Muslim Brotherhood," he told reporters.
Shater, the Brotherhood's number two who headed its financial affairs, is behind bars and on trial for a range of charges, some of them punishable by death.
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He was arrested along with Brotherhood chief Mohamed Badie following the ouster of Morsi in July 2013.
Seoudi is a wealthy businessman but little is known about his role in the Muslim Brotherhood.
The movement, which swept all elections since the fall of strongman Hosni Mubarak up to the election of Morsi in June 2012, was blacklisted in December as a "terrorist group" by the military-installed authorities.
Morsi was ousted by then army chief Abdel Fattah al-Sisi following mass protests against his one year rule. Last month Sisi was elected as president in a landslide victory.
Soon after his ouster, the authorities closed several television stations and a Brotherhood-run newspaper.
The two medium-sized supermarket chains had operations in Cairo, selling food and beverages.
Dozens of masked policemen were seen stopping customers from entering a Seoudi outlet in central Cairo on Sunday.