The visit assumes significance for expansion of trade ties as well with various countries of Asia Pacific region and Singh held bilateral meetings with Prime Ministers of Asian superpowers like Japan and Australia as well on the sidelines of Asean and East Asia Summits in Brunei.
Singh also announced a separate mission for Asean, a 10-member block of South East Asian nations, with a full time ambassador.
Besides, he also said that a Free Trade Agreement on services and investments would be signed with Asean by end of 2013 to help meet India-Asean trade to USD 100 billion by 2015.
Singh was in Brunei Darussalam from October 9-10 for attending Asean Summit as also the East Asia Sumit, a forum for co-operation among Asean nations and its partner countries that include China, India, Australia, Japan and the US.
After Brunei, Singh came to Jakarta on October 10 for his first official bilateral visit to Indonesia, although he has been here thrice for multi-lateral and regional events.
Six pacts were signed between India and Indonesia including in areas like health, anti corruption, narcotics, disaster management and academics.
Two leaders agreed to expand their strategic partnership by holding annual summits and an eminent persons group will be set up to expand the relationship.
New areas of co-operation have been identified such as space, nuclear energy, food security, counter-terrorism, transborder threats from jehadi forces.
Co-operation will be expanded in areas like defence, maritime and a comprehensive action plan will be developed for security cooperation.
The Indian delegation in Indonesia also included External Affairs Minister Salman Khurshid, Commerce and Industry Minister Anand Sharma and Chief Vigilance Commissioner Pradeep Kumar, besides other top officials.
Singh also participated in a wreath laying ceremony at Kalibata Heroes' cemetery here and was given an official welcome in the Medekera Palace courtyard. He also signed guest book at the palace before his meeting with Indonesian President Susilo Bambang Yudhohono.
Last night, a state banquet was also hosted by president and his wife Ani Bambang Yudhohono at Negara Palace for Singh and the Indian delegation.
Officials said that relationships with Asean and other Asian countries are now moving towards more strategic partnerships as areas of cooperation have expanded from only economic issues to security, defence, intelligence sharing etc.
Even on trade, the relations would grow multi-fold after the FTA on services and investments is signed with Asean later this year and gets implemented by July 2014.
Asean leaders now expect to strengthen the security dimension of cooperation with India, officials said about Singh's meetings in the two countries.
Six pacts were signed between India and Indonesia.
The issue of maritime security was also discussed by various leaders, while other areas where cooperation is expected to increase include counter terrorism measures, non traditional security threats and disaster mitigation and management.
On South China sea dispute, India made its position clear that the freedom of navigation should be there as per international norms and an early resolution should be worked by first making early progress towards adoption of Code of Conduct norms.
Asked about a different approach taken by China on this issue, officials said India was very clear on its position irrespective of any other country's view.
They said that there were certainly some differences among countries on the issue of sovereignty but India was firm on its stance that these issues should be resolved through consultations as per the international norms.