Rafsanjani, 82, died of a cardiac arrest caused by heart attack.
He died in a state-run hospital in the Iranian capital on Sunday.
The Supreme Leader expressed regret in his message over the 'sad and sudden demise' of 'Sheikh Akbar Hashemi Rafsanjani,' to whom the Leader referred to as an 'old friend, a companion in the course of the campaign during the Islamic movement days and a close colleague.'
Ayatollah Khamenei also pointed to the long record of the late Ayatollah's campaigns and cooperation in the past 59 years.
The Supreme Leader said the loss is 'so hard and heart rending' for him.
'His high intelligence and unprecedented sincerity for the (59) years was a safe backing for all his colleague, me in particular,' the message said.
Rafsanjani, a veteran Iranian cleric and politician served in different posts in the post-1979 Islamic Revolution era.
He was Iran's president between 1989 and 1997.