They were discovered near the border and have been evacuated by helicopter to receive medical treatment.
Fighting between rival forces in July left hundreds of people dead less than a year after a peace deal was signed.
Mr Machar, who had joined a unity government, fled - and was also aided by the UN in DR Congo a few weeks ago.
South Sudan has suffered more than two years of civil war since gaining independence from Sudan in 2011.
Political differences between Mr Machar and President Salva Kiir ignited a civil war in December 2013 - and they only agreed to settle their differences under intense international pressure, signing a peace deal in August 2015.
Mr Machar returned to Juba in April but battles then broke out between his bodyguards and presidential guards in South Sudan's capital, Juba, in July.
Mr Machar fled Juba in the wake of the July clashes and was later dismissed as vice-president.
After receiving medical treatment in DR Congo in August, he was flown to Sudan's capital, Khartoum, where he remains after being discharged from hospital.
His soldiers, who had crossed into DR Congo, were found in an area around the Garamba National Park by UN peacekeepers, UN spokesman Stephane Dujarric said.
He said they had suffered mostly from walking in difficult terrain and having no access to food.
Many were in critical condition and were helped "on purely humanitarian grounds so that they can receive urgent medical assistance", Mr Dujarric said.
An internal Congolese army report, seen by the Reuters news agency on Wednesday, said 500 fighters were evacuated to Goma in the middle of August - a mission that involved three flights a day over three days.
More on South Sudan's crisis:
Following UN pressure last week, President Kiir has now agreed to the deployment of a 4,000-strong regional protection force for Juba which would have a more robust mandate than the 12,000 UN soldiers already in the country, however the mandate and size of the force still have to be agreed.
This was a key request of Mr Machar, who said he wanted a neutral force to guarantee his safety.
But US officials are now saying that they do not believe Mr Machar should return to his post.
"Given all that has happened, we do not believe it would be wise for Machar to return to his previous position in Juba," US special envoy Donald Booth told a congressional subcommittee on Wednesday.
"But this cannot become a justification for President Kiir to monopolise power and stifle dissenting political voices," Reuters quoted him as saying.
Meanwhile, the UK is to send an extra 100 troops to South Sudan, joining the 300 already serving in the UN peacekeeping force there.
More than 100 fighters loyal to South Sudan's sacked vice-president have been found "in extremely bad shape" by the UN in the Democratic Republic of Congo.