The move came hours after Sirisena suspended Parliament till November 16 after Wickremesinghe sought an emergency session to prove his majority.
The President withdrew Wickremesinghe's personal security and vehicles in order to accord them to his 72-year-old successor Rajapaksa, who staged a dramatic political comeback on Friday.
Sirisena would address the nation on Sunday while the new Cabinet will be announced on Monday, government sources said.
The Rajapaksa camp was busy making transition preparations despite the constitutional question mark on the legality of Wickremesinghe's sacking.
The ousted premier said that he still commands the majority in the 225-member assembly.
Rajapaksa and Sirisena combine has only 95 seats and is short of a simple majority in the 225-member house. Wickremesinghe's United National Party (UNP) has 106 seats on its own with just seven short of the majority.
The UNP claimed that President Sirisena sought to prorogue the parliament as 72-year-old Rajapaksa did not command a majority in the House.
Veteran civil servant S Amarasekera was named Rajapaksa's secretary by Sirisena after sacking Wickremesinghe's secretary Saman Ekanayake, a government gazette said.
The Rajapaksa camp said that they would seize the prime minister's official residence cum office known as the Temple Trees if Wickremesinghe did not quit by Sunday.
They have already started running the prime minister's secretariat with Amarasekera's appointment.
Meanwhile, China's Ambassador in Colombo Cheng Xueya became the first Ambassador to greet Rajapaksa with best wishes.
Cheng said he was bringing good wishes from Chinese President Xi Jinping.
Wickremesinghe, meanwhile, held a briefing for the Colombo-based Ambassadors to explain the situation, his officials said.
In another development, Dharisha Bastiansz, the editor of the state organ Sunday Observer said in a tweet that she had been forced to leave the editorial team by Rajapaksa-supported trade unions.
"Today I had to leave Lake House (publishing house), unable to carry out my editorial duties," she tweeted.
Rajapaksa's loyalists took control of the state TV stations on Friday night itself after he took oath as the new prime minister.