"The President had telephoned Mr Sharif from Uganda to offer his congratulations on the electoral victory," presidential spokesman Mohan Samaranayake said today.
Rajapaksa is on a 4-day official visit to Kampala.
Sri Lanka regards Pakistan as a close ally in the region with cooperation coming from its South Asian neighbour during the island's armed conflict with the LTTE.
Meanwhile the Pakistan High Commission here today announced the arrival of a Pakistani Naval ship equipped with multi role missiles and other modern weapon systems in Sri Lanka's eastern port of Trincomalee.