When the president's allies formally announced Mr Yar'Adua's arrival home - they pointedly referred to Mr Jonathan as the "vice-president", appearing to strip him of this acting president role.
Then a group claiming to speak for Mr Jonathan hit back with a statement calling him "acting president" three times.
The BBC's Caroline Duffield in the capital, Abuja, says Nigerian politics is always murky - but that difference in title clearly matters.
And there are now few rules to guide what happens next, she says.
Mr Yar'Adua's condition is unknown and he has not been seen in public since 23 November.
"We do not think he has the capacity today. We are appealing to him, and his handlers, that he should honourably resign his appointment," Osita Okechukwu of the Conference of Nigeria Political Parties, a group representing opposition parties, told the BBC.
But our reporter says the president's tight-knit circle have bought him home for a reason.
Analysts say that the struggle for the leadership is really about money.
Whoever holds power also has access to a patronage machine - oiled by billions of dollars from the Niger Delta.
That is a prize that many people are willing to fight for, our correspondent says.