Palestinian medical sources said the two teenagers were killed on Friday near a Jewish settlement in the Gaza Strip.
The two were later named by family sources as Muhammad Khalaf and Muhammad al-Ashqar. Both were reportedly members of the resistance group Al-Aqsa Martyrs Brigades.
Another Palestinian was shot dead by Israeli troops in the Hebron region of the southern West Bank, witnesses and Palestinian security sources said.
The killings coincided with an invasion of the West Bank town of Bethlehem by Israeli troops.
The Israelis have staged a partial pull-out from the city since then.
The two Palestinian teenagers were killed when Israeli troops opened fire at a group of men who were approaching the Jewish settlement in northern Gaza.
"We have identified a few armed figures approaching the community of Dugit. They were around 150 metres from the community, armed with an RPG and an explosive," an Israeli military source claimed. "We identified a hit."
The other Palestinian killed in Hebron was identified as Jihad al-Sweiti.
Wanted by the Israelis, he was shot dead when a gun battle broke out while Israeli soldiers tried to arrest him from a house where he had taken refuge.
The latest deaths bring the overall toll since the start of the Palestinian intifada in September 2000 to 3370, including 2788 Palestinians and 875 Israelis.
Aljazeera's correspondent in Ram Allah, Shireen Abu Akla reported that Israeli occupation troops overnight invaded Bethlehem in armoured vehicles, entering the town from various crossings in the villages of al-Khudhr, Bait Jala and Bait Sahour.
"The occupation forces carried out search campaigns in al-Dihaisha refugee camp in the city," Akla reported.
Bethlehem is one of the few places in the occupied West Bank that the Israeli army had evacuated and handed over to the Palestinian Authority.
A few hours later, the Israelis staged a partial withdrawal, but maintained a presence in the adjoining Ayda refugee camp.
On Thursday morning a bomber from Bethlehem blew himself up in a bus in west Jerusalem near the Israeli prime minister's residence, killing 10 people and wounding dozens.
After the pullback, Palestinian security services returned to their headquarters in the town and policemen returned to street patrols.
An Israeli military spokesman said the army "was continuing its activities" in the Bethlehem region but said that operations had been scaled down.
Israeli sources said some arrests had been made, without giving figures.