It was 10pm in Washington DC when Mr Joyce announced his resignation from the front bench and the party leadership, and he still had not directly spoken to the Prime Minister on his decision.
"I look forward now obviously to working with the new leader of the National Party who will be elected on Monday", Mr Turnbull said.
Joyce, who confirmed he will be stepping down as deputy prime minister, sent Twitter into a frenzy after repeatedly using a term it seems no one could understand. Amid pressure from his own party, the member for New England said on Friday he would remain in the seat but would move to the backbench. "I think it's gotta stop for the poor buggers who're parked outside my house every day, they've gotta go home".
The Nationals President Larry Anthony said the party had greeted the news of Joyce's resignation with "a heavy heart", The Guardian reported.
Mr Joyce put himself on a collision-course with Mr Turnbull last Friday, when he launched an extraordinary attack on the Prime Minister, calling his comments on the affair "inept", "unnecessary" and "hurtful".
The coalition government is in crisis with a public row between Joyce and the PM stepping up a notch.
Earlier this month, the former deputy prime minister had withstood a parliamentary vote Thursday that would have called for his firing after revelations of a relationship with a former staffer and a free-residence deal with a wealthy political donor. Joyce had asked for the allegation to be referred to police, the spokesman said.
Joyce had spent the past week on "holiday" in Armidale, though he made a number of media appearances, including a candid interview with his partner and former media advisor, Vikki Campion.
Joyce has been leader of the Nationals and deputy prime minister since February 2016.
The affair has also spurred a debate about what parts of a parliamentarian's life are private and should be off-limits to media reporting. John McVeigh MP will act as Minister for Infrastructure and Transport. He has always lead from the front and his colleagues and our party membership always knew who he was fighting for in Canberra.
Mr Turnbull explained that Mr Joyce was taking leave to consider his future.
"Barnaby has made mistakes but I am sure he will recover, learn and be a better person from them", Canavan said.