Mr Bennett was scheduled to make his first state visit to India this week but it was cancelled after the Israeli leader tested positive for Covid-19.
“Was happy to speak with PM Naftali Bennett and to know that he is recovering well. We discussed recent global events, and also reviewed India-Israel co-operation in various areas,” Mr Modi tweeted after his telephonic call.
Mr Modi offered his condolences over the five deaths in a terrorist attack in Israel's capital Tel Aviv, India’s Foreign Ministry said.
India and Israel are this year marking the 30th anniversary of establishing diplomatic relations between the two nations.
“It was great speaking to you my friend, @NarendraModi. I look forward to seeing you soon!” Mr Bennett tweeted after his call with Mr Modi.
The two nations have strengthened bilateral ties in recent decades, particularly since Mr Modi came to power in the world’s largest democracy.
Mr Modi made a historic visit to Israel in 2017 — the first official visit there by an Indian prime minister — a significant move by New Delhi that for decades was seen as pursuing a largely pro-Palestine policy.
India was the only non-Arab country among the 13 which in 1948 voted against the creation of Israel as a separate state under the UN partition plan of Palestine in the General Assembly.
India recognised Israel two years later and formally established diplomatic relations in January 1992 when it opened its embassy in Tel Aviv.
For decades, India had maintained a tense balancing act between Israel and Palestine.
But after Mr Modi’s right-wing Bharatiya Janata Party came to power in 2014, New Delhi gradually decoupled the Israel-Palestine issue and bolstered its relationship with Tel Aviv, particularly in defence and strategic areas.
India has used the terms “natural allies” and “strategic partners” to describe the relationship between the two nations.
New Delhi in recent years has abstained from UN resolutions condemning Israel.
It did so last month, abstaining from voting at the UN Human Rights Council that condemned Israeli actions in the occupied Palestinian territories.
India is Israel's third largest trading partner in Asia and the bilateral trade has diversified into several sectors including pharmaceuticals, agriculture, IT and telecoms, and homeland security.
The bilateral merchandise trade between the countries stood at $5.65 billion dollars in 2018-2019.
The two countries have for years been working to deepen co-operation on defence and information technology.
India is Israel’s biggest market for military hardware and supplies various weapon systems, missiles and technology. It had supplied arms to India during the Kargil war with Pakistan in 1999.
There are also routine exchanges between the armed forces of the two countries.
Last year, the Indian government was accused of illegally using an Israeli surveillance spyware Pegasus to snoop on an array of opposition leaders, journalists, academics and retired and serving government bureaucrats.
Mr Modi’s government has given vague replies on the purchase and use of the spyware by his administration but a committee is looking into the allegations after the Supreme Court ordered a probe last year.