Jaishankar spoke after the boycott said terrorism was a deliberate obstacle to regional cooperation.
Jaishankar left the meeting after his speech and avoided coming face-to-face with Qureshi.
The official Twitter account of Pakistan Tehreek-e-Insaaf, the ruling party, said of the boycott, "Pakistan will not engage with the butcher of Kashmir."
Qureshi later returned to the meeting and spoke.
The meeting was presided over by Nepal, the current head of the South Asian Association for Regional Cooperation and its other foreign ministers from Afghanistan, Bangladesh, Bhutan, Maldives, Nepal and Sri Lanka participated.
In his speech, Jaishankar said, "Ours is really not just a story of missed opportunities but also of deliberate obstacles. Terrorism is among them."
"In our view, elimination of terrorism in all its forms is a precondition not only for fruitful cooperation but also for the very survival of our region itself," he said.
He said the region's nations should instead work together to bring prosperity to the people.
"The example of South Asian Satellite shows how India has been taking up the initiatives that bear prosperity to the neighbourhood. South Asian satellite was launched in 2017 with an intention to arrive at scientific solutions to address poverty in the SAARC region," he said.
Last year, the late External Affairs Minister Sushma Swaraj left the SAARC ministerial meeting held on the sidelines of the United Nations General Assembly after her speech.
Later speaking at a think tank, Qureshi undiplomatically made crude personal comments about her.
Interactions between India and Pakistan at the SARC has been strained because of Islamabad's backing for terrorism.
India refused to participate in the SAARC summit in 2016 in Pakistan after a terrorist attack on an Army base in Kashmir. It was cancelled after Afghanistan, Bangladesh and Bhutan also decided not to attend.
(Arul Louis can be contacted at arul.l@.in and followed on Twitter @arulouis)
( With inputs from IANS )