Singh called up Raje, who is set to become chief minister of Rajasthan, and wished her well, PMO sources said.
Raje led BJP to an emphatic victory in the assembly elections, ousting Congress from power.
The Prime Minister also called up Chouhan and Raman Singh to wish them well, the sources said.
Chouhan, chief minister of Madhya Pradesh, spearheaded BJP in retaining power in the state for the third consecutive time with an increased tally in the assembly.
Raman Singh, chief minister of Chhattisgarh, also led his party in retaining power.