Morocco recalled its ambassador from South Africa in 2004 after former South African President Thabo Mbeki recognized a breakaway region in the Western Sahara, which Morocco claims as part of its territory.
"Morocco is an African nation and we need to have relations with them," Zuma told City Press in the interview. "We never had problems with them anyway; they were the first to withdraw diplomatic relations."
Zuma met Morocco's King Mohammed last week on the sidelines of an African Union-European Union summit.
"They felt that even if we differ on the Western Sahara issues, the two countries should have a relationship," Zuma said about Moroccan officials' position at the meeting.
South Africa's official government position - as re-affirmed by Zuma in one of his state of the nation addresses - is to support "self-determination and decolonization for the Western Sahara".
The decision to re-establish ties with Morocco is likely to go down badly with some members of South Africa's ruling African National Congress (ANC), of which Zuma is leader.
The ANC - as one of Africa's oldest liberation movements - has long backed those seeking independence in the Western Sahara and has accused Morocco of occupying the region.
The ruling party said in a statement it had "unequivocal support for Western Sahara" but that this did not mean it harbored enmity towards Morocco.
"There is also no ANC policy that says South Africa should isolate Morocco," the statement said.
A spokesman for South Africa's foreign ministry could not be reached for comment on Sunday.
Morocco has controlled most of the Western Sahara, which is rich in phosphates and has seen some initial oil exploration efforts, since 1975. A ceasefire in 1991 called for a referendum on self-determination for Western Sahara, but the vote has never taken place.