South Sudan leader Salva Kiir is to seek re-election in that post rather than tackling Omar al-Bashir for the national presidency, his party says.
The SPLM will instead field a northern Muslim, Yasir Arman, in the national elections due in April.
The BBC's James Copnall in Khartoum says this is where the party's priorities lie - in the south.
The SPLM ended its two-decade war with the north in 2005 and joined a unity government but tensions are high.
A referendum is due next year on whether the oil-rich south should become independent.
The April poll will be the first national elections in 24 years.
Our correspondent says more than three-quarters of the population live in the north, so it is likely that a northern candidate will win the election.
Mr Kiir also does not have the broad national support the late SPLM leader John Garang enjoyed, our reporter says.