The Prime Minister also wished him "well for the future."
Siddaramaiah was yesterday elected as the leader of the Congress Legislative Party in the state.
"Prime Minister Manmohan Singh talked to Siddaramaiah to congratulate him on his election as the Chief Minister of Karnataka and to wish him well for the future," the PMO said.
The 64-year-old backward class leader was chosen yesterday in Bangalore at a meeting of the newly-elected MLAs in the presence of four AICC observers headed by Defence Minister A K Antony.
The Congress picked Siddaramaiah to be the new chief minister after a secret poll of its legislators.
He edged out party veteran and Union Labour Minister M Mallikarjuna Kharge in a hotly-contested race.
Siddaramaiah is credited with leading the Congress party's battle against the BJP government in the state.