Motlanthe, overwhelmingly elected in a secret ballot, replaces Thabo Mbeki, who resigned on Sunday after nine years in power.
Almost one-third of South Africa’s cabinet stepped down on Tuesday out of loyalty to Mbeki, who presided over South Africa’s longest period of economic growth.
Motlanthe said the new government would not change economic policy but would intensify efforts to create more jobs.
"In a turbulent global economy, we will remain true to the policies that have kept South Africa steady, and that have ensured sustained growth," he said in a speech prepared for delivery, after parliament elected him interim president.
Motlanthe, a quiet spoken leftist intellectual and ally of Zuma, faces huge challenges including slowing economic growth and high inflation. Officials said on Thursday consumer inflation hit its highest level since before the end of apartheid in August, at 13.7 percent.
Reflecting the ANC’s dominance of parliament, Motlanthe won 269 votes from members of parliament, compared to 50 for the candidate of the opposition Democratic Alliance.
ANC parliamentarians greeted the announcement of the vote with cheers and clapping.
The upheaval in the ANC, climax of a power struggle between Mbeki and Zuma, has raised concerns of instability in Africa’s biggest economy and a possible split in the formerly monolithic ruling party.
"The ANC for some time has spoken about the need to maintain the (economic) policies that have been in place, so as things stand now, one shouldn’t necessarily expect a major policy change," said Leon Myburgh, sub-Saharan specialist at Citigroup.
"Motlanthe himself of course has always been a bit of a quiet, behind the scenes figure, so the next few months will be interesting to monitor him, and what he says and his actions."
In a sign of the wounds, parliamentary officials said Mbeki would not attend Motlanthe’s swearing-in later on Thursday despite being invited.
It was not immediately clear when Motlanthe would name his new cabinet although investors are keenly watching to see if highly respected Finance Minister Trevor Manuel will be reappointed.
Motlanthe, a former mine union leader and anti-apartheid soldier, is widely respected by both radical leftists and business tycoons within the African National Congress.
He will try to heal the worst rifts in the history of the party because of the battle between Mbeki and Zuma, which has overshadowed pressing issues such as widespread poverty and crime and an AIDS epidemic ravaging millions.
Radical policy changes under Motlanthe in the short transitional period are unlikely but foreign investors eager for stability and a continuity of economic policy will be watching closely for clues on whether the ANC will change course.
The populist Zuma is trying to reassure foreign investors he would not stray from business-friendly economic policies but is under pressure from left-leaning union allies to alleviate poverty through more government spending. Reuters