At least 18 civilians, 17 government soldiers and two soldiers from Nkunda's brigade were wounded in the gun battle, UN officials said.
Two government soldiers were killed in the clashes, the government said.
The clashes are less than one week after the Democratic Republic of Congo (DRC) held its first multiparty elections in more than 40 years, aimed at cementing peace after a 1998-2003 war during which Nkunda rebelled against Kinshasa.
The UN said there was nothing to worry about after a deal was reached between Commanders of Nkunda's fighters and the army's 9th brigade to withdraw both forces from the town.
But women carrying children on their backs and men bearing suitcases or mattresses walked in long lines along the road to the provincial capital Goma, 20 kms (13 miles) to the east, near to the Rwandan border.
"The firing has stopped. There are fears and apprehensions. There was a small misunderstanding but there is nothing to worry about," Brigadier General GV Satyanarayana, commander of United Nations forces in North Kivu, told Reuters in Sake.
U.N. peacekeepers - part of a 17,000-strong force in Congo - were patrolling Sake to prevent further hostilities.
President Laurent Kabila, widely credited with securing the 2003 peace deal, was favourite to win the vote but results are not expected for more than two weeks and opposition leaders have alleged fraud.
People chanted "Vote Kabila! Vote Kabila!" in support of the president, as UN forces arrived.
"We are singing for Kabila because he is the only one who will bring peace," said Sake resident Faustin Kasolu, 38.
Nkunda, from the Tutsi ethnic group found in Rwanda, Burundi and Congo, is the subject of an international arrest warrant issued by the Congolese government for alleged atrocities against civilians committed since 2004.
He said last week that he was willing to negotiate with the winner of Sunday's historic elections to end his resistance, but also warned he would fight back if a new elected president tried to defeat him militarily.