"What's happening is that one part of unity government, the MDC, can travel all they want, around the world and do what they want while the other part, the Zanu-PF, cannot," Zuma said on Friday.
"That's impeding the functioning of the unity government and so the international community that supported the power-sharing agreement must also lift the sanctions to allow the unity government to function to its full capacity."
Both the European Union and the US maintain a travel ban and asset freeze on Mugabe, his wife and inner circle in protest at disputed 2008 elections and alleged human rights abuses by his government.
A power-sharing agreement between Zanu-PF and MDC has failed to make major headway since it was installed two years ago.
Zuma, who has urged Western powers to lift sanction in the past, said that should sanctions be lifted "we can make faster progress".
Yoweri Museveni, the Ugandan president, endorsed Zuma's position in a joint statement.
Zimbabwe has been mired in a political and economic crisis for years, with much of its economic woes blamed on Mugabe's policies.
Zuma was in Uganda as part of a delegation of cabinet ministers and business men.
While there he and his host also discussed the situation in Democratic Republic of Congo.
In a statement they said they had agreed that while security there was improving, the United Nations' peacekeeping mission there, known as Monuc, was still needed to provide stability.