Gaza Health Ministry spokesman Ashraf al-Kidra said the militants' car was hit in an airstrike. The men were members of the Popular Resistance Committee, a militant group aligned with Gaza's Hamas rulers that often fires rockets at Israel, he said.
Gaza militants have fired 30 rockets at Israel since the search for the teens began, including one that exploded inside Gaza killing a Palestinian girl earlier this week.
Israel's Defense Minister Moshe Yaalon confirmed the strike on the militants. "Aircraft killed a terror operative inGaza who had been responsible for recent rocket attacks on southern Israel and was planning more terror attacks on Israeli citizens," he said in a statement. Israel considers Hamas responsible for what happens in Gazaand warned the group not to "test Israel's patience and determination" he said.
Earlier, Israel's military says it fired at Hamas targets in Gaza after an explosive device was deployed against troops on the border, causing no injuries. A Palestinian boy was seriously hurt in the fire.
The incidents came as Israel's operation in search of three teens feared abducted in the West Bank entered its third week.
Israel blames Hamas, which controls Gaza, for the teen's abduction. On Thursday, it identified two well-known Hamas operatives in the West Bank as the central suspects. Hamas has praised the abduction of the teens but not taken responsibility for it.
The three teens — Eyal Yifrah, 19, Gilad Shaar, 16, and Naftali Fraenkel, a 16-year-old with dual Israeli-American citizenship — have not been heard from since hitchhiking home in the West Bank on June 12.
Israel launched its broadest ground operation in the West Bank in nearly a decade following their disappearance, arresting about 400 Palestinians, most of them Hamas activists.
Israel's Shin Bet security service named the suspects as Marwan Qawasmeh and Amer Abu Aisheh. It said both men are Hamas activists in the West Bank city of Hebron, near where the youths disappeared. Hamas in Hebron has confirmed the two suspects are members of the group.
Israeli and Palestinian officials said the two men have been missing since the teenagers disappeared and a manhunt is underway.
Abu Aisheh's mother, Nadia, told the Associated Press that "If it's Amer as they say, I will be proud of him until I die and be by beside him."
Also Friday, scores of protesters clashed with police in the Arab town of Umm al-Fahm in northern Israel.
The mostly Arab protesters called for an end to the Israeli operation to locate the teens and crackdown on Hamas in the West Bank.
Israeli media reported that some reportedly called for more abductions. Foreign Minister Avigdor Lieberman called on police to arrest them for incitement.
Israel's Arab minority enjoys full citizenship rights. Some complain of discrimination and the group for the most part identifies with the Palestinians.
Copyright 2014 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.