The authorities suppressed a similar protest last week
Sudanese police have fired tear gas at stone-throwing protesters, who were demanding democratic reform.
Unconfirmed reports say dozens of protesters were arrested during the clashes, in the city of Omdurman.
The violence came a day after rival parties agreed rules for a national election and a referendum on southern independence due in the next two years.
The north and south fought a two-decade civil war which ended in 2005, when both sides agreed to share power.
The deal saw President Omar al-Bashir's National Congress Party (NCP) going into government with former rebels from the south.
But leaders of the ex-rebel Sudan People's Liberation Movement (SPLM) have repeatedly expressed fears that Mr Bashir's supporters were trying to sabotage the votes to retain power over the whole country.
Southern leaders have been seeking changes to electoral laws which they believe would have allowed the NCP to rig the votes - and at the weekend they appeared to have sealed a deal.
However, many of the details of the agreement have not been released and both sides need it approved by their parties.
Senior figures held
The protest Omdurman, just across the River Nile from Khartoum, had been planned by the SPLM and northern opposition parties well before Sunday's deal was announced.
The BBC's James Copnall in Omdurman says hundreds of demonstrators gathered at the headquarters of one of the parties organising the rally, intending to march to parliament.
They chanted slogans about freedom and justice, but riot police stopped them about 100m up the road firing tear gas, our correspondent says.
The opposition Ummah party told the AFP news agency that one of its senior members had been arrested - though there was no confirmation of their claim.
Last week similar protests in Khartoum and Omdurman were suppressed by the authorities, who said the demonstrators had not gained the proper permits.
Several senior SPLM officials were briefly detained by police during that rally, raising concerns about its participation in the power-sharing government.
Analysts say the build-up to next April's national election appears to have galvanised opposition to Mr Bashir's rule.
The protests have been organised by southern politicians, but the northern opposition has been increasingly involved.