Jones, who arrived here last evening after a tour of Afghanistan and Pakistan, met the Prime Minister at his Race Course Road office here.
The US National Security Adviser is in the country to hold high-level consultations with the Indian leadership and top diplomats on the situation in South Asia.
The visit of Jones comes ahead of US Secretary of State Hillary Clinton's tour of India scheduled next month.
Jones had met his Indian counterpart M K Narayanan yesterday during which they are believed to have discussed the security situation in the region with focus on Pakistan and Afghanistan.
He is scheduled to have another round of talks with Narayanan and will also have a meeting with Defence Minister A K Antony.
This is the first high-level visit by an US official after India and Pakistan agreed to discuss the steps taken by Islamabad against terrorism directed against New Delhi.
In Islamabad, Jones met Pakistan Army chief Gen Ashfaq Kayani and is understood to have taken stock of the ongoing military operations against the Taliban in northwest Pakistan and discussed American troop surge in Afghanistan.
Deccan Herald is on WhatsApp Channels| Join now for Breaking News & Editor's Picks