He described Fernandes' death as a ''personal loss''.
Fernandes (80), a former Union Minister and Rajya Sabha member, died at a private hospital in Mangaluru on Monday.
He was hospitalised in July after he suffered a head injury due to a fall while practising yoga at his home. He had also undergone a surgery to remove a clot in his brain.
''My heartfelt condolences to the family and friends of Shri Oscar Fernandes Ji. It is a personal loss for me. He was a guide and mentor to many of us in the Congress party,'' Gandhi said on Twitter.
''He will be missed and fondly remembered for his contributions,'' he added.
Fernandes was a sitting member of the Rajya Sabha from Karnataka. He had been a five-time Lok Sabha MP and a four-time Rajya Sabha member.
He had entered politics as a member of the Udupi Municipal Council and was elected to Lok Sabha for the first time in 1980.
Fernandes became the parliamentary secretary to the prime minister in December 1984 and then the AICC general secretary in 1985. Thereafter, he became the president of Karnataka Pradesh Congress in 1986 and AICC general secretary from 1996 onwards.