Prime Minister Malcolm Turnbull told parliament that Mr Joyce would not fill his post as acting leader next week. Mr Turnbull is due to travel to the US.
Mr Joyce has faced questions over whether he followed ministerial rules.
The scandal has gripped Australian politics since last week.
Mr Joyce's relationship with his former media adviser, Vikki Campion, was revealed publicly last Wednesday.
He has denied that he breached a ministerial code of conduct over two unadvertised jobs within his party that were offered to Ms Campion last year.
Mr Turnbull said Mr Joyce would be on leave for a week from Monday. The high-profile conservative had only returned to parliament in December after briefly losing his job over his New Zealand dual citizenship.
It's unlike Barnaby Joyce to step away from the front line. He's a hardened battler who normally revels in the noisy confrontation of politics.
Mr Joyce is the man who took on Johnny Depp, a man he called a "dipstick", and won; the politician who survived the citizenship row and was re-elected with an increased majority.
The man in the Akubra hat was riding high until his extramarital affair was exposed and he lost authority within his own party.
With the storm around him showing no sign of slowing, Mr Joyce will hope his impromptu holiday can somehow calm matters.
But his opponents are unlikely to stop sniping, just because he's taken cover.
Under the code of conduct, Mr Turnbull must approve any ministerial department job given to the partner of a frontbencher. No permission was sought for Ms Campion.
However, both Mr Joyce and Mr Turnbull maintain that Ms Campion was not the deputy prime minister's partner at the time of the appointments.
Mr Joyce was due to step in as acting prime minister while Mr Turnbull was away, in line with usual convention.
The role will instead be taken up by Mathias Cormann, the government's leader in the Senate.
Opposition parties stepped up their attacks on Mr Joyce on Thursday, calling on him to resign.
Mr Joyce has also faced scrutiny over other revelations arising from the scandal.
On Thursday, opponents questioned whether Mr Joyce had misled parliament over "the gift" of his current residential address - an apartment owned by a businessman.
The Labor opposition, citing official standards, argued that ministers "must not seek or encourage any form of gift in their personal capacity". Mr Joyce denies he sought or encouraged the gift of the apartment.
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