"The two sides identified issues relating to bilateral trade and deliberated upon the future roadmap in order to enhance trade and economic co-operation," it said.
Indian Commerce and Industry Minister Kamal Nath inaugurated the meeting on Tuesday. Commerce Secretary Tasneem Noorani led the Pakistani delegation, while his Indian counterpart S.N. Menon represented his side.
The statement said the terms of reference for the sub-groups were mutually agreed upon.
The JSG had detailed discussions on promotion of the trade and economic co-operation for mutual benefit of both countries, said the statement, adding the talks were held in a cordial and constructive atmosphere.
The JSG recommendations would be submitted to the respective governments for consideration under the framework of the composite dialogue, it added.
At the conclusion of the first meeting, it was decided to hold the second JSG meeting on mutually agreed dates.
Trade between the two countries has been hit by decades of hostility centred around their dispute over Kashmir. Direct trade is worth only about $300 million a year - a fraction of their combined $200 billion trade with the world.
Trade through third countries is, however, estimated to be 10 times higher than direct trade. Analysts say there is immense potential for more direct trade as the countries make cautious progress towards peace.
If they showed the right flexibility, trade could grow five-fold in a couple of years, Indian Commerce and Industry Minister Kamal Nath said on Tuesday.
"An improvement in the political atmosphere will move trade and commerce forward between two countries. Both should move in tandem," Commerce Secretary Tanseem Noorani told a news conference.
"There are several obstacles to trade between the two countries. Our objective is to remove all these barriers," he said, adding that there was no timeframe for the panels to submit reports.
According to government statistics, India's exports to Pakistan swelled by a record 328 percent in April-July to $167 million from $39 million in the same period a year ago.
At that pace, bilateral trade may surpass $500 million by March 31.
The agreement came as Afghan President Hamid Karzai said he had proposed a trade corridor for Indian exports to Afghanistan through Pakistan and would push the idea further with Islamabad.
Karzai arrived in New Delhi on Wednesday for a three-day visit. He raised the possibility of a trade corridor in talks with Indian Foreign Minister Natwar Singh, the Indian foreign ministry said in a statement.