The Council of Scientific and Industrial Research awarded Natarajan the Shanti Swarup Bhatnagar Prize, one of the highest Indian science awards, in 1984. He received the Best Teacher Award from the Government of Tamil Nadu the same year. In 1999, he was awarded the Acharya P.C. Ray Memorial Award by the Indian Chemical Society. He held the National Lectureship and the National Fellowship of the University Grants Commission of India during 1986–87 and 1989–91 respectively. Sir M. Visweshwaraiah Chair of the University of Mysore (1999), Pandit Jawaharlal Nehru Chair of the University of Hyderabad (2004), Raja Ramanna Fellowship of the Department of Science and Technology (2006–09) and the senior scientist professorship of the Indian National Science Academy (at the time of his death) were some of the other notable positions he held. He was an elected fellow of the Indian Academy of Sciences, Indian National Science Academy, International Union of Pure and Applied Chemistry, Tamil Nadu Academy of Sciences, Society of Bio-Sciences and Gujarat Academy of Sciences and a member of Sigma Xi: The Scientific Research Society.