Accompanied by BJP chief Amit Shah, the PM also visited Mr Advani's Delhi residence to wish him early on Tuesday morning. Amit Shah tweeted photographs from the meeting.
PM Modi said in tweets,
Wishing our inspiration, one of India's tallest leaders who has served India tirelessly & diligently, Shri LK Advani ji on his birthday.Narendra Modi (@narendramodi) 8 November 2016
I pray to God that Advani ji is blessed with a long and healthy life.Narendra Modi (@narendramodi) 8 November 2016
Many ministers and senior leaders have tweeted their wishes to Mr Advani, who turns 89 today.
LK Advani, for years one of the most powerful men in the BJP, gave Narendra Modi his first big breaks in the party. Mr Advani's famous rath yatra in 1990 from Somnath in Gujarat to Ayodhya in Uttar Pradesh, was organised by his protege.
But they fell out over the years and the BJP's win in the 2014 national election under PM Modi's leadership brought an end to what was called the Vajpayee-Advani era in the party.
The Narendra Modi-Amit Shah era had begun. Three months after PM Modi took office with the biggest mandate in 30 years, he effected a revamp within the BJP, relegating Mr Advani to an advisory committee of mentors, the "marg-darshak mandal," described by the opposition as a "retirement home."
Mr Advani was effectively removed from crucial decision-making groups in the party.
The relationship between the two leaders, which had reportedly begun to unravel more than ten years ago, was at its most bitter as PM Modi was elevated in the party before the 2014 election. LK Advani, who once served as India's deputy PM and is said to have nursed the ambition of becoming Prime Minister, vehemently opposed the decision to pick then Gujarat Chief Minister Narendra Modi as presumptive PM.
After the elections, Mr Advani was denied the post he wanted - that of Parliament Speaker.
He came out of quasi retirement last year to join hands with other party seniors in blaming PM Modi and party chief Shah for the BJP's crushing defeat in the Bihar elections.
But earlier this year, he had praise for the Prime Minister when he said, as the government celebrated two years in power, "India has received an honest government at the centre under Prime Minister Narendra Modi."
PM Modi's government, he said, was "moving in the right direction."