The injured ambassador Burhan Muhammad was airlifted here from Islamabad after being seriously injured in the crash in Pakistan-occupied Kashmir's Gilgit-Baltistan in the north that also killed his wife Heri Listyawati.
Envoys of the Philippines and Norway and the wife of Malaysian ambassador besides two army pilots and a Pakistani crew member were also among those killed in the May 8 crash that was claimed by the Taliban.
"Indonesia's foreign ministry has just lost one of its best diplomats, Ambassador Burhan Muhammad, who passed away at 00:50 on May 19 local time in Singapore," foreign minister Retno Marsudi said.
Prime Minister Sharif has expressed deep grief and sorrow over his death, Radio Pakistan reported.
Sharif lauded the late ambassador's role in promoting friendship between Indonesia and Pakistan and prayed that the Almighty may bless the departed soul with eternal bliss and grant courage to the bereaved family to bear this loss with fortitude.
The Tehreek-e-Taliban Pakistan (TTP) claimed responsibility for the downing of the chopper, saying Prime Minister Nawaz Sharif was their target.
They also released a video later, showing its militants with a surface-to-air missile which it claimed was used to bring down the army helicopter.
Pakistan Army, however, ruled out the possibility of any terrorist or subversive activity in the crash and said the chopper crashed due to a technical fault while landing.
The air crash, the worst since 2012 when a civilian 737 went down in Islamabad killing 130 people, was also reminiscent of the one in 1988 that killed then military-ruler General Zia-ul-Haq as well as the US ambassador at the time Arnold Raphel.
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