Striking good personal chemistry, the two leaders had "very fruitful" and "meaningful" exchanges after which Abe announced doubling of Japan's private and public investment in India to about USD 35 billion over the next five years.
The talks at Akasaka Palace (State Guest House) came on the third day of Modi's first major bilateral visit outside South Asia. Abe had gone the extra mile in receiving his old friend in Kyoto on Saturday and spent the weekend with him on a tour of two ancient Buddhist temples apart from hosting a banquet.
Significantly, at an interaction with business leaders, Modi deplored the "expansionist" tendencies among countries which "engage in encroachment" and "intrude" into the seas of others, comments seen as a veiled reference to China.
At the summit talks, the two countries decided to elevate their ties to a Special Strategic Global Partnership, emphasising that a developed India and a prosperous Japan was important for Asia and for global peace and security.
"This is not just raising the relationship from one category to another... Our relationship is not only regional in its framework, but will have a global impact," Modi, who is on a five-day visit to Japan, said.
While agreeing on greater defence equipment and technology cooperation, the two sides decided to expedite discussions on modalities for the sale of Japanese US-2 amphibian aircraft.
"The two Prime Ministers reaffirmed the importance of defence relations between India and Japan in their strategic partnership and decided to upgrade and strengthen them," a joint statement issued after the talks said. On the civil nuclear deal over which there were expectations of it being finalised during the visit, both Modi and Abe said they have directed the officials to accelerate negotiations for early conclusion of a bilateral agreement to strengthen their partnership.
While India is said to be pursuing the deal with Japan on the template of the landmark Indo-US nuclear accord, Tokyo is said to be not that enthusiastic about that being the basis.
The joint statement while making a reference to nuclear ties said, "In recent months, we have made significant progress in our negotiations on civil nuclear cooperation. Today, we have discussed this issue at length. We have reached better understanding of each other's positions through this discussion.
"We have agreed to instruct our negotiators to work expeditiously to conclude the negotiations at an early date so that we can further strengthen our strategic partnership," it added.
The 3.5 trillion yen( 35 billion USD) of investment from Japan to India including Official Development Assistance(ODA) during a 5-year period will be under the aegis of IndiaJapan Investment Promotion Partnership for development of projects including infrastructure and building smart cities.
The five-year period will also see the doubling of the presence of Japanese firms in India, Abe said.
Abe also announced that as an example of Indo-Japan cooperation, Tokyo will help India in providing financial, technical and operational support to introduce Bullet trains, a project that Modi has been actively pursuing.
Coinciding with the summit, Japan removed six of Indias space and defence-related entities from its Foreign End User List.
Modi appreciated this decision and said both the countries are looking forward to enhanced trade and collaboration in high-end technology.
The six companies removed from Japan's end user list can now enter into transactions involving sensitive dual-use equipment, technology and software.
"We have to decide if we want to have 'vikas vaad' (development) or 'vistar vaad' (expansionism) which leads to disintegration. Those who follow the path of Buddha and have faith on 'vikas vaad', they develop. But we see, those having ideas of the 18th century, engage in encroachments and enter seas (of others)," Modi said at the business event.
He did not name any country but the comments may be seen as targeting China which is engaged in territorial disputes with a number of its neighbours, including India, Japan and some others including Vietnam.
Thanking Abe for providing him an opportunity to make Japan his first bilateral visit outside South Asia, Modi said," we both have decided to raise the relationship to a special strategic and global partnership by giving it a special emphasis".
Asserting that his visit ushered in a dawn of new era in Indo-Japan relations, Modi said there is no "limit" to partnership between the two countries.
Modi also said that Japan occupies top priority in India's foreign policy.
He was effusive in his praise for Abe saying he spent a considerable amount of his valuable time to be with him in Kyoto for two days and in Tokyo today.
The Prime Minister said Abe has agreed to cooperate with India in all areas taking into account his vision of inclusive development of the country.
"We will help you," Abe told Modi, adding he was ready to extend his help in Ganga cleaning project when he raised the issue.
"This is an example of his love and respect for India," he said, adding the relationship between the two countries was also spiritual in nature.