The 27th amendment, passed by a two-thirds majority, also consolidates military power under a new Chief of Defence Forces role and establishes a Federal Constitutional Court.
The changes grant army chief Asim Munir, promoted to field marshal after Pakistan's clash with India in May, command over the army, air force and the navy.
He and other top military brass will enjoy lifelong protections.
Under the amendment, any officer promoted to field marshal, marshal of the air force, or admiral of the fleet will now retain rank and privileges for life, remain in uniform, and enjoy immunity from criminal proceedings.
Such protections were previously only reserved for the head of state.
"This constitutional amendment will increase authoritarianism and whatever little semblance of democracy existed in this country will fade away," said Osama Malik, an Islamabad-based lawyer.
"It will not only remove civilian oversight from the military's activities, it will also completely destroy the military hierarchy where all service chiefs were considered equal under the joint chief system," he told AFP.
Pakistan, a nuclear-armed nation of more than 250 million people, has long struggled to balance civilian authority with the military's role in politics.
The amendment also shields President Asif Ali Zardari from any criminal prosecution, although that immunity will not apply if he or any other former president later holds another public office.
Zardari has faced multiple graft cases, although proceedings were previously stayed.
He signed the bill into law following the parliamentary vote.
- 'Deeply undemocratic' -
Opposition parties, led by the Pakistan Tehreek-e-Insaf (PTI), tore up copies of the bill in both chambers over the past few days.
The amendment also bars courts from questioning any constitutional change "on any ground whatsoever".
The bill also creates a Federal Constitutional Court with exclusive jurisdiction over constitutional cases, stripping the Supreme Court of its original powers and transferring pending petitions.
Another clause empowers the president to transfer High Court judges on the recommendation of the Judicial Commission, a change critics say could be used to sideline dissenting judges.
"This is the final nail in the coffin of an independent judiciary and a functioning democracy," PTI spokesman Sayed Zulfiqar Bukhari told AFP.
PTI secretary general Salman Akram Raja described the amendment as "deeply undemocratic at its core".
"They have given lifetime immunity from criminal prosecution to the president and created a system that concentrates power in one military office," he told AFP.
The Senate initially passed the bill on Monday. It was then tweaked and passed by the National Assembly, the lower house, two days later before returning to the upper house for final approval.
"Sixty-four members are in favour of the passage of the bill and four members are against, so the motion is carried," Senate Chairman Yusuf Raza Gilani said on Thursday.
It also cleared the 336-member lower house with the required two-thirds majority.
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