But annual Russia-India trade has slipped below $10 billion since 2014, as Modi cultivated closer diplomatic and economic ties with Washington, while Russia has courted Pakistan and China.
USA officials have said there is no guarantee of a waiver from the Trump administration, which has imposed sanctions on China's military for the purchase of the same system.
"In today's fast-changing world, our relationship assumes heightened importance", Modi told Putin.
India has signed more than $15 billion in USA defence contracts since 2008, including for C-130J and C-17 transport aircraft, P-8I maritime patrol aircraft, Harpoon missiles and Apache and Chinook helicopters.
Describing Russia as a traditional ally, the Prime Minister said a special cell has been set up here to facilitate investments from Russia into India.
India and Russian Federation on Friday also signed a document for cooperation to implement new nuclear power project (NPP) following talks between Modi and Putin.
The deal has been an issue of much speculation after US President Donald Trump's administration's law - Countering America's Adversaries Through Sanctions Act (CAATSA) - came into effect in January.
The long-range missile systems will bolster India's air-defence capabilities along the 4,000-km-long India-China border.
The dinner meeting comes a day ahead of the 19th India-Russia annual summit during which the two leaders will hold comprehensive discussions on wide-ranging bilateral, regional and global issues, including USA sanctions against Moscow and counter-terrorism cooperation.
Last month Washington slapped financial sanctions on the Chinese military for buying Russian Sukhoi Su-35 fighter jets - and the S-400. For all the warm words, ties with Moscow are a lot less central to Delhi than they were during the Cold War years, as India has diversified arms purchases, closing $15 billion of deals with the United States over the last decade.
Analysts say Washington's response to the India-Russia deal will be a major determining factor of the future of US-India relations.
The Russian President is accompanied by a high-level delegation comprising Deputy Prime Minister Yuri Borisov, Foreign Minister Sergey Lavrov and Trade and Industry Minister Denis Manturov among others during his two-day visit.
The US has hinted at tough sanctions against any nation that buys advanced military hardware from Russian Federation. "India gives the highest priority to ties with Russian Federation, in fact in a changing world, our ties have become more important", Modi said.
After the summit, Modi spoke of a "trusted" and "special and privileged partnership" with Moscow as he addressed reporters along with Putin.
Moscow has been New Delhi's largest defense supplier since the 1960s, accounting for 68 percent of India's arms imports from 2012 to 2016, according to the Stockholm International Peace Research Institute (SIPRI).