The army said that the youth killed Friday had been about to hurl a petrol bomb at Israeli motorists near the West Bank city of Ramallah.
An army spokesperson said troops posted at the village of Silwad to protect a major road widely used by Jewish settlers in the occupied territory spotted a person about to hurl a petrol bomb.
"The forces fired immediately to neutralise the danger... and confirmed a hit," she said.
Palestinian officials named the youth as Orwa Hammad, 17, saying he was shot during a stone-throwing protest against troops, a regular occurrence at Silwad, near Ofra settlement.
US State Department spokesperson Jen Psaki said the US "expresses its deepest condolences to the family of a US citizen minor who was killed by the Israeli Defense Forces".
Calling for "a speedy and transparent investigation", Psaki said officials from the US consulate in Jerusalem were in touch with the family of the slain youth.
"We continue to urge all parties to help restore calm and avoid escalating tensions in the wake of the tragic recent incidents in Jerusalem and the West Bank," said Psaki.
Locals in Silwad said Hammad's father lives in the United States.
Also on Friday, police in annexed east Jerusalem clashed with Palestinians, firing tear gas to disperse stone-throwing protesters.
They were deployed in force ahead of weekly Muslim prayers as the army restricted access to a flashpoint mosque, after a deadly Palestinian attack sent tensions soaring.
Clashes have broken out nightly since a Palestinian ploughed his car into a crowd of Israelis on Wednesday, killing a baby who Washington said was a US citizen, and injuring six other people before he was shot dead by police.
The security presence was boosted across east Jerusalem including the Old City, police spokeswoman Luba Samri said.
Palestinian men under the age of 40 were not allowed into Jerusalem's Al Aqsa mosque compound for Friday prayers because of fears of further unrest, she said.
The compound is the scene of frequent clashes between Palestinians and Israeli police.
The plaza houses the Dome of the Rock and Al Aqsa mosque, Islam's third-holiest site. It is also revered by Jews as the location of the biblical Jewish temples, considered Judaism's holiest place.
Prayers concluded on Friday afternoon with clashes in the Wadi Joz neighbourhood north of the Old City.
Palestinians there threw stones and fired flares at police, who dispersed them and arrested three demonstrators, Samri said.
An AFP correspondent said undercover police in the crowd of Palestinians made the arrests.
There were also clashes in east Jerusalem's Issawiya neighbourhood, where AFP photographers saw police fire bursts of tear gas to break up a crowd of Palestinians who hurled rocks and burned tyres on the streets.
There were no reports of injuries on either side.
Samri said around 8,000 people took part in prayers at Al-Aqsa, with hundreds of others in areas around the site.
On Thursday night, two Palestinians were arrested during clashes in the Old City in which stones, bottles and flares were thrown or fired at police, who used unspecified "riot dispersal" weapons, Samri said.
The fighting has shaken east Jerusalem on an almost daily basis since the murder of a Palestinian teenager by Jewish extremists in July.
Clashes intensified during the 50-day Gaza war.
Police branded Wednesday's incident - in which 21-year-old Abdelrahman Shaludi from Silwan in east Jerusalem drove at high speed into a crowd of Israelis - a "terror attack".
Silwan - a densely populated Arab neighbourhood on a steep hillside just south of the Old City - has been the focus of Palestinian anger over Jewish settlements in east Jerusalem.
Prime Minister Benjamin Netanyahu has warned that any further attacks would be met with "the harshest response".
Meanwhile a suicide car bomb attack in the Sinai peninsula which killed 30 Egyptian soldiers prompted Cairo to close the Rafah crossing into the Gaza Strip, the only route into the Palestinian territory not controlled by Israel.
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