The famous national monument, named Ziarat Residency, was where Jinnah spent his last days in 1948.
The separatist Baloch Liberation Front militant group destroyed the historic building in June 2013, sending shockwaves across the country.
Sharif government had decided to restore the building in its original shape and after initial estimates, the real work started four months ago.
The residency was restored at a cost of Rs 150 million but Sharif waited to inaugurate it on Pakistan's Independence Day.
He was accompanied by army chief General Raheel Sharif, governor and chief minister of Balochistan and several other officials.
Located in Ziarat, the wooden building was first built during the British Raj in 1892 as a sanatorium, but was later converted into the summer resort of the agent of the governor general.
Jinnah being terminally ill in 1948 was advised by doctors to shift to Ziarat near Karachi for its temperate climate which his ailing body needed.
He spent last two months and ten days in this building before being shifted to Karachi where he died.
