On Friday, the army said it had used unspecified "means of dispersing demonstrations" against some 250 violent protesters taking part in a weekly rally against the fence near the West Bank village of Bilin.
Photos showed clouds of tear gas billowing around stone-throwing protesters.
Palestinian Prime Minister Salam Fayyad also attended Friday's Bilin protest but was unhurt.
"We condemn this abominable crime by the Israeli occupation army in Bilin against people taking part in a peaceful demonstration and consider it an Israeli war crime against our people," Palestinian chief negotiator Saeb Erakat told AFP.
The hospital did not say if Abu Rahma suffered from asthma or any other condition that could have aggravated the effects of the gas.
At her funeral in Bilin on Saturday, about 3,000 mourners accompanied her body, which was draped in a Palestinian flag.
Her mother Subhiya, 64, clutched a picture of her daughter and sobbed.
"Jawaher asked to be a martyr; now she is a martyr," she said.
Acquaintances said the dead woman's brother, Bassem Abu Rahma, was killed during an April 2009 protest at the same site, when he was hit on the head by a tear gas canister fired at close range.
Another brother, Ashraf, was filmed by activists being shot in the leg with a rubber-coated bullet by a soldier while he was bound and blindfolded in the aftermath of a 2008 anti-barrier protest at the village of Nilin, near Bilin.
The video was widely distributed and caused a media storm, leading two years later to the conviction for "unbecoming conduct" of the soldier and an officer who was present at the time.
Palestinians joined by Israeli and foreign activists protesting against Israel's construction of the West Bank barrier have clashed with soldiers nearly every Friday outside Bilin and Nilin for years.
Nearly 200 demonstrators gathered in Tel Aviv on Saturday to protest against Abu Rahma's death. A dozen people were arrested, an AFP correspondent reported.
Israel says the projected 723 kilometres (454 miles) of steel and concrete walls, fences and barbed wire is needed for security. The Palestinians view it as a land grab that undermines their promised state.
The International Court of Justice (ICJ) issued a non-binding ruling in 2004 calling for parts of the barrier inside the West Bank to be torn down and for further construction in the territory to cease.
Israel has ignored the ruling.
The demonstrations are billed as non-violent but frequently turn into clashes between rock-throwing Palestinian youths and Israeli troops firing tear gas and rubber-coated bullets.
When completed, 85 percent of the wall will have been built inside the West Bank, taking land from villages like Bilin and Nilin.
In February, Israel began work on rerouting a part of the barrier near Bilin more than two years after a Supreme Court order, moving it hundreds of metres (yards) to the west.
The Supreme Court ruled in September 2007 that the barrier in the Bilin area was "highly prejudicial" to the villagers and demanded that the government map out an alternative route "within a reasonable period."