Mr Johnson shocked his party by announcing his immediate departure and resignation from his Uxbridge and South Ruislip seat.
Despite the former Prime Minister’s attack on the Privileges Committee and its upcoming report on Partygate, Mr Shapps told Sky News Mr Johnson was “perfectly entitled” to stay on as an MP but standing down was his decision.
The Energy Secretary added: “I liked working with him as Prime Minister, but the world has moved on.
“He is the one who’s removed himself from the current political scene, standing down as a member of Parliament.”
In his resignation on Friday, Mr Johnson claimed a House of Commons inquiry was determined to find him guilty over Partygate.
He then said there had been a “witch hunt” among some Tory MPs who saw his removal as a necessary first step to the reversal of Brexit before saying he was sad to be leaving Parliament “for now”.
When asked whether he agreed with Sir Jake Berry, an ally of the former Prime Minister, that the “establishment” was in charge rather than voters, Mr Shapps said: “No, actually in the end Boris was perfectly entitled to remain as an MP.
“He has decided to step down and a couple of my other colleagues, all of them whom I’ve worked with and Boris in particular, I liked working with him as prime minister.
“But … the world has moved on. He is the one who has removed himself from the current political scene, standing down as a member of Parliament.
“We’ve got excellent leadership in place in No 10 with Rishi Sunak.”
Mr Johnson’s former Downing Street communications director, Guto Harri, said he now expects his former boss to “lick his wounds” and that the resignations are not “part of an elaborate plot to sort of destabilise and topple” Mr Sunak.