Senior rebel official Nyarji Roman said James Gatdet Dak had been arrested at his Nairobi home on Wednesday and taken to the airport 24 hours later.
He was sent back to the South Sudanese capital Juba where he was immediately detained, according to Roman, a spokesman for the rebel SPLM/A-IO.
Machar telephoned Kenya's deputy president, William Ruto, in a bid to halt Gatdet's deportation on the grounds of "profound fear for his life" but the spokesman was sent back anyway, Roman said.
"The deportation of Mr. James Gatdet Dak is a violation of the Geneva Convention," Roman added, saying an intervention by the UN refugee agency had failed to prevent the move.
"Moreover, the Kenyan government is a guarantor to the peace agreement that was signed in August 2015 and we do not expect that it would put in danger the life of an innocent person."
That viewpoint was shared by Gerry Simpson, a senior refugee researcher at Human Rights Watch.
"In colluding with South Sudan and deporting James Gatdet Dak, Kenya has exposed him to a serious risk of persecution," said Simpson.
South Sudan President Salva Kiir's spokesman Ateny Wek Ateny also confirmed that Gatdet was back in the country, refusing to comment further.
"Obviously the key element we would like to emphasise right now is that this person needs to have his rights protected and his wellbeing ensured by the government," Geneva-based UNHCR spokeswoman Cecile Pouilly said.
South Sudan's rebels warned that Kenya could face repercussions over the deportation.
"This can inadvertently put in danger Kenyan NGOs' workers in (rebel-held) areas in South Sudan," said the SPLM/A-IO representative to the United Nations, Miyong G. Kuon.
On the run
Just before his arrest, Gatdet had expressed his support for the sacking of a Kenyan general of a United Nations peacekeeping force accused of failing to protect civilians during a fresh outbreak of violence in Juba in July.
Kenya has responded to Tuesday's sacking of lieutenant general Johnson Ondieki by announcing it will pull its 1,050 troops out of South Sudan and drop plans to contribute soldiers to a planned UN regional force for Juba.
According to South Sudanese radio station Tamazuj, a delegation of Kenyan MPs was visiting South Sudan on Friday and expressed their opposition to the rebels.
"We will discourage anybody trying to use our country as a launching pad for war," said Asman Kamama, the Kenyan chair for national security.
Violence between Machar's supporters and troops loyal to his bitter political foe, President Salva Kiir, has blighted South Sudan for much of its hard-won independence from Sudan, achieved in 2011.
South Sudan descended into war just two and a half years later when Kiir in December 2013 accused Machar -- whom he had sacked as his deputy -- of plotting a coup.
The war has left tens of thousands of people dead and forced nearly two million people to flee their homes.
Machar himself fled South Sudan following July's clashes between his rebel fighters and Kiir's government forces, and has been on the run ever since, turning up variously in the Democratic Republic of Congo, Sudan and South Africa.
A return to Ethiopia, where he lived during previous peace negotiations, was ruled out by that country's prime minister, Hailemariam Desalegn, who said in September: "We do not need someone who is leading an armed struggle in Ethiopia."
Machar's naming as a vice-president was a key condition of a hard-won peace deal signed in August 2015 which is now in tatters.