The Department of International Relations and Cooperation released a short statement on Monday saying Zuma had “congratulated the President of Uganda for holding peaceful elections and committed to working with the Government of Uganda to strengthen bilateral relations between the two countries”.
But commentators and election monitors have been sceptical of the election.
Uganda’s electoral commission has come under fire after hundreds of thousands of voters in opposition strongholds were not allowed to vote.
In power for 30 years‚ Museveni’s National Resistance Movement won 60.8% of the vote‚ against 35.4% for Kizza Besigye’s Forum for Democratic Change.
Besigye has rejected the results.
He was detained and placed under house arrest during the poll‚ after he threatened to demonstrate that there were discrepancies in the numbers.
Many polling stations where the opposition were expected to win received their polling materials too late for all those present to vote.
The electoral commission announced the results before 1800 polling station results were factored in.
Ugandan civil society groups have criticised the commission‚ as have observers from the European Community and the US