Mr Machar fled Juba at the start of the conflict in December 2013.
More than two million people have been displaced and tens of thousands killed in the fighting.
Head of the rebel negotiating team Taban Deng told the BBC that Mr Machar would still go to Juba on Monday but he would now be sworn in as vice-president in the evening, not in the morning as planned.
He said the delay was because a second plane was needed for Mr Machar`s army chief, who had been due to travel on Sunday.
Earlier, rebel spokesman William Ezekiel told journalists waiting for Mr Machar at Juba`s airport that the trip had been postponed until Tuesday.
He said that the rebels were still committed to the peace process agreed last August.
The government has not yet responded to the delay.
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