The Ministry of Foreign Affairs said in a statement that this step is a setback in the path towards coexistence and just peace.
Pakistan's Prime Minister Shahid Khaqan Abbasi arrived in the Afghan capital Kabul on Friday on a one-day visit aimed at improving relations between the countries.
The final statement declared "East Jerusalem as the capital of the State of Palestine" and invited "all countries to recognise the State of Palestine and East Jerusalem as its occupied capital."
The attack, which came as US envoy Jason Greenblatt was in Jerusalem for talks on relaunching the moribund Middle East peace process, drew condemnation from Israeli officials.
After an exhausting two days in Saudi Arabia, US President Donald Trump arrived in Israel on Monday, attempting to revive the stalled Israeli-Palestinian peace process with visits to Jerusalem and the West Bank.
Palestinian President Mahmoud Abbas landed in New Delhi late on Sunday for a three-day visit looking to strengthen ties with India ahead of Prime Minister Narendra Modi's historic trip to Israel.
Pro-government forces pushed a fierce bid to recapture Syria's ancient city of Palmyra from jihadists on Thursday as Moscow hosted top US diplomat John Kerry for talks on the fraught peace process.
Afghan security forces killed a team of suicide bombers who targeted the Indian consulate in the eastern city of Jalalabad, following an attack in which at least six people were wounded, officials said.