A visit to Mr Thackeray's residence 'Matoshree' in suburban Bandra was not in Mr Kovind's itinerary which had raised eyebrows.
However, he made a phone call to Mr Thackeray and thanked him for supporting his candidature for the July 17 presidential election, Shiv Sena sources said.
Mr Kovind held a meeting with elected representatives of the BJP, the Shiv Sena and other NDA allies at the Garware Club in south Mumbai.
Pranab Mukherjee and Pratibha Patil, as presidential candidates of the UPA, had visited the then Shiv Sena chief Bal Thackeray at 'Matoshree' as the party had broken ranks with the NDA in the past two elections for the highest constitutional office.
Mr Thackeray had announced his party's support for Mr Kovind after a meeting of Shiv Sena leaders here last month.