The one-to-one meeting between Krishna and Khar was followed by delegation-level talks between the two sides.
Indian officials earlier said that terrorism will form the core of New Delhi's discussions, particularly the slow pace of the Mumbai attack case trial.
Other issues include those concerning prisoners as well as trade and border issues. The talks will culminate in inking of much-awaited new liberalised visa agreement to boost people-to-people contacts.
For the first time, group tourism will be part of the new pact which will also have other new categories, including multiple city one-year visas for businessmen and visa-on-arrival for people aged 65 years.
Foreign Secretary Ranjan Mathai and his Pakistani counterpart Jalil Abbas Jilani were also present.
Both Ministers will also co-chair the Joint Commission Meeting later this evening, which was revived in 2005 after a gap of 16 years. This is Krishna's second visit to Pakistan in over two years.
Ahead of today's meeting with Khar, Krishna yesterday called on President Asif Ali Zardari and Prime Minister Raja Pervez Ashraf and met a series of political leaders from MQM, ANP and PML-Q parties.
Also, Foreign Secretary-level talks were held yesterday here during which the two sides discussed all aspects of the resumed dialogue, apart from reviewing the entire expanse of the discussions held so far.
The two sides described their discussions as "positive" and "frank". They acknowledged that progress has been made in bilateral ties but agreed that "much more needs to be done".
Later today, the two sides will also ink an agreement on culture between Indian Council of Cultural Relations (ICCR) and its Pakistani counterpart PNCS.