First, the absence of the almost regulatory parallel visit made by nearly all visiting statesmen to Palestinian President Mahmoud Abbas in Ramallah.
The second was the fact that for nearly the entire visit, Mr Modi's host, Prime Minister Benjamin Netanyahu, did not leave his side.
Beyond the historic aspect – it was the first visit of a serving Indian prime minister (Mr Modi visited once before as a BJP MP in 2006), and marked 25 years since the two countries established diplomatic relations - it sets in stone a shift in India's previously pro-Arab foreign policy and the obvious personal affinity between the two leaders.
Officially, the business side of the visit was the signing of seven agreements on civilian cooperation in fields of water desalination, agriculture, technology and space exploration, but the foundation of the burgeoning alliance, the ongoing security and military cooperation, was never far from the surface.
Upon landing at Ben-Gurion Airport, Mr Modi said that "alongside building a partnership for shared economic prosperity, we are also cooperating to secure our societies against common threats such as terrorism".
What he did not mention is that India is now Israel's largest market for arms exports, amounting to over a billion dollars a year in missile, radar and avionics sales. Israel is currently India's third-largest foreign supplier of weapon systems.
Leaving out Ramallah from the visit was no coincidence. Palestinian Deputy Foreign Minister Tasir Jaradat chided Mr Modi saying on Al Jazeera, saying that "to play an important role between the two sides and to be able to spread the message of peace, one should visit both.”
In recent years, under the BJP government, India's voting record at the United Nations, which was once consistently pro-Palestinian, has changed.
Mr Modi, like Israel's PM, a right-wing hardliner who styles himself as an outsider who overcame the old political establishment in his country, has been anxious not to include anything in the visit that could offend or irk his host. Before coming to Israel he said India still supported a two-state solution but that such a solution should be "a final agreement (which) must recognise the feelings and demands of all sides involved".
Mr Netanyahu has been working since his return to office in 2009 to establish warmer relations with the emerging super-powers in the Far East, putting a specific emphasis on India.
To this end, Mr Modi - who is almost his age and shares a large part of his worldview, with the exception of India's extensive commercial dealings with Iran - has been a central partner since his own election in May 2014.
