Kovind gave his assent yesterday to the recommendation by the Election Commission (EC).
Reacting to the development, senior AAP leader Ashutosh said, "President's order to disqualify AAP MLAs is unconstitutional and dangerous for democracy."
The Election Commission (EC) had on Friday recommended to Kovind that the 20 MLAs were liable for disqualification for holding offices of profit between March 13, 2015, and September 8, 2016.
AAP MLAs were appointed parliamentary secretaries and this was described by petitioner Prashant Patel as them holding offices of profit.
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Parliamentary Secretaries assist ministers with their work. AAP insisted that despite holding the office these MLAs did not take any salaries or perks.
The President is bound by the recommendation of the Commission. Under the rules, petitions to the President seeking disqualification of lawmakers are referred to the EC. The poll panel takes a decision and sends its recommendation to the Rashtrapati Bhavan which is accepted.
The Commission had said that it is basing its opinion on judicial pronouncements of the past, the Government of National Capital Territory of Delhi Act and the Constitution.
The 20 MLAs disqualified include, Adarsh Shastri (Dwarka), Alka Lamba (Chandni Chowk), Anil Bajpai (Gandhi Nagar), Avtar Singh (Kalkaji), Kailash Gahlot (Najafgarh) -- who is also a minister -- Madan Lal (Kasturba Nagar), Manoj Kumar (Kondli), Naresh Yadav (Mehrauli), Nitin Tyagi (Laxmi Nagar), Praveen Kumar (Jangpura).
The AAP had also approached the Delhi High Court seeking a stay on EC's recommendation. The court has listed the case for a hearing on Monday.
On Friday, the Delhi High Court had refused to pass any interim order of protection to AAP MLAs from being disqualified.
Madanlal, one of the 20 disqualified MLAs, said that all hopes now hinge on the judiciary and the party was expecting some relief tomorrow.
Once the vacancies are announced by the Assembly, the AAP's strength would go down to 46 from 66 in the 70-member House. However, it will continue to have a majority to run the state.
"We are expecting relief from the court. Our petition is coming up for hearing tomorrow," Madanlal, who represented the Kasturba Nagar constituency, said.
Alka Lamba, who is among the 20 AAP MLAs disqualified, said the decision was "painful" and the president should have heard them out before arriving at any conclusion.