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"The agreement will facilitate movement between the two countries, this is part of the guarantee that government gave to FIFA," spokesperson Ronnie Mamoepa told Sapa.
He said the department hoped to sign similar agreements with other countries in the Southern African Development Community.
Dlamini-Zuma and her Mozambican counterpart Jose Pacheco signed the agreement in Pretoria.
It would take effect on Tuesday until the end of the tournament on July 11.
"The objective of the agreement is to expedite the entry and exit of visitors from both countries for the duration of the 2010 Fifa World Cup through the Lebombo/Ressano Garcia border post."
The agreement would allow both countries to co-ordinate their joint border clearance and the prevention and detection of immigration control offences.