Nadine Dorries, the culture secretary and arch ally of the Prime Minister, angrily denied suggestions Mr Johnson was working to boost Liz Truss’s campaign for No 10.
Ms Truss, the foreign secretary, is being backed by Mr Johnson’s allies and is seen as the most likely challenger to face Rishi Sunak in the run-off if she can overcome Ms Mordaunt, who has so far come second in voting among Tory MPs.
Mr Ellwood, a former minister who chairs the Commons Defence Committee, argued he was unable to travel back from a meeting with the president of Moldova because of “unprecedented disruption”.
But a Tory source said: “Other Conservative MPs cancelled foreign trips, left poorly relatives, and one MP’s mother died on the morning of the vote, and still attended and voted.”
Sir Graham Brady, the chairman of the 1922 Committee of backbench Tories in charge of the leadership election, confirmed those who lose the Tory whip, meaning they are kicked out of the parliamentary party, can no longer vote in the race.
With Mr Johnson’s move coming ahead of the penultimate round of voting by Tory MPs on Tuesday afternoon, it prompted speculation he was working for the benefit of Ms Truss’s campaign.
But Ms Dorries wrote on Twitter: “This is wholly untrue and frankly utterly ridiculous.
“Every single MP of every party is under no illusion regarding the price to be paid in not voting during a Gov confidence motion. It’s a very clearly defined and historic red line. Tobias could have voted like everyone else.”
MPs voted 349 to 238, majority 111, to support the motion stating the Commons has confidence in the Government, but Mr Ellwood’s name appeared on the no vote recorded list alongside 11 other Conservative MPs.
A spokeswoman for the Tory whips’ office said: “Tobias Ellwood MP has lost the Conservative Party whip following his failure to vote in support of the Government in the confidence vote last night.”
A Conservative source said the other Tories who appeared on the list with Mr Ellwood were appropriately paired with other MPs for the purpose of the vote, giving them a valid excuse not to.
Mr Ellwood, who was first elected in 2005 as Conservative MP for Bournemouth East, said he had been unable to return from a meeting with Moldovan president Maia Sandu in the nation’s capital of Chisinau, near the Ukrainian port city of Odesa.
“Following my meeting yesterday with the President of Moldova I was unable to secure return travel due to unprecedented disruption both here and in the UK,” Mr Ellwood said in a statement.
“I am very sorry to lose the whip, but will now continue my meetings in Ukraine promoting the Prime Minister’s efforts here and specifically seeking to secure the re-opening of Odesa port – so vital grain exports can recommence.”
The Tory source said Mr Ellwood did not seek formal permission to go on the trip after his permission slip not to attend the vote was revoked.
Mr Johnson called the confidence vote after Labour launched its own challenge to try to force the Prime Minister to leave office immediately.
The victory means he is expected to continue in Downing Street until September, when Tory members choose the winner from the final two leadership candidates selected by Tory MPs.
Liberal Democrat Chief Whip Wendy Chamberlain said: “It is telling that Boris Johnson acted swiftly to punish Tobias Ellwood this time, but dragged his feet for days when it came to suspending the whip from his loyal supporter Chris Pincher.
“This petty act shows there is no room in the Conservatives any more for those who refuse to prop up Johnson.
“The Conservative leadership candidates should condemn this move and make clear they will restore the whip to Tobias Ellwood.”