It was the first deadly airstrike in Gaza since a truce was reached with Palestinian militants last November, and is the most serious test yet of the Egyptian-brokered agreement.
The strike came alongside the fatal stabbing of an Israeli settler in the West Bank, the first killing by a Palestinian of an Israeli in the territory in over a year.
The aircraft hit the motorcycle as it was traveling northwest of Gaza City, killing the driver and wounding a passenger. A bystander was also wounded, according to Gaza medical officials.
The Israeli military said it had successfully killed Haitham Mishal, whom it said was a jihadi militant involved in an April 17 rocket attack on the southern Israeli resort town of Eilat and other violence. Ashraf al-Kidra, Gaza's Health Ministry spokesman, said Mishal was a policeman.
Israeli Prime Minister Benjamin Netanyahu had warned in recent days that Israel would not tolerate rocket fire from either the Gaza Strip or Egypt's Sinai desert.
"We hit today one of those involved in the despicable rocket fire on Eilat. I said that we would not be quiet over that," Netanyahu said Tuesday. "We do not accept sporadic rocket fire from Gaza or Sinai. We will act to protect the citizens of Israel, and we are acting."
Tuesday's airstrike may strain a five-month-old cease fire brokered by Egypt last November that ended eight days of heavy fighting between Israel and Hamas. Under the deal, Gaza militants pledged to halt rocket attacks on Israel, while Israel said it would end its policy of assassinating wanted militants.
But after months of calm, the truce has begun to unravel. Palestinian militants have sporadically fired rockets into open areas of southern Israel in recent weeks. The Israeli air force has responded with strikes on training sites and suspected weapons storage sites in Gaza. Until Tuesday, there had been no casualties.
In a statement, the Israeli military said Mishal had been involved in the Mujahideen Shura Council in the Environs of Jerusalem, a murky al-Qaida-inspired group that has claimed responsibility for a number of rocket attacks, including the Eilat incident.
Israel viewed the rocket attack on Eilat, a normally tranquil oasis that borders the Red Sea and Egypt's Sinai desert, as an escalation. It accused Gaza militants of firing the rockets, which caused no injuries, out of Egypt's lawless Sinai desert.
It said Mishal "has been a key terror figure, specializing in weapons and working with all of the terror organizations in the Gaza Strip." It said he manufactured weapons and specialized in rockets and explosive devices that he sold to militant groups.
Hamas, the Islamic militant group that rules Gaza, condemned the Israeli attack but also signaled that it is eager to preserve the truce.
"We call on Egypt to put pressure on the Israeli occupation to stop these crimes and to force them to honor the truce and stop the aggression," said Hamas spokesman Fawzi Barhoum. He called for a "joint and unified" effort by Gaza's various militant factions.
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Hamas considers the jihadi groups responsible for recent rocket fire to be rivals, and has struggled to keep them in check. Since the cease-fire was reached, Hamas has deployed security forces along the border areas with Israel and Egypt to help preserve the calm.
In the West Bank, meanwhile, a Palestinian man fatally stabbed an Israeli waiting at a bus stop and fired on police before he was detained by Israeli security forces, officials said.
The victim was identified as a 32-year-old man from a nearby West Bank settlement. The attack took place at an intersection in the northern West Bank, near the Palestinian city of Nablus.
Israeli police spokesman Micky Rosenfeld said the assailant stabbed the Israeli and took his gun, then opened fire at border police nearby. The officers returned fire, wounding the Palestinian who was then detained. The Israeli man died of his wounds at the scene, Rosenfeld said.
Netanyahu latter expressed sorrow over the stabbing. "The terrorist who committed this murder was captured and we will continue to operate on that front to protect our citizens," he said.
A militant group claiming affiliation with the Al Aqsa Martyrs' Brigades, a violent offshoot of Palestinian President Mahmoud Abbas' Fatah, movement took responsibility for the stabbing attack in notices posted on the Internet.
The group said it had "received a green light to begin a series of operations against the (Israeli) occupiers" in response to the deaths of two Palestinians in Israeli jail earlier this year. Abbas, an outspoken critic of violence, did not immediately comment.
The stabbing was the first fatal attack on Israelis in the West Bank since September 2011. But Capt. Barak Raz, a military spokesman, said the area has experienced a rise in rock throwings and firebombings in recent months. A baby Israeli girl was seriously injured earlier this year when Palestinians threw rocks at the car she was traveling in. Palestinians charge that some settlers, particularly in smaller remote hilltop communities, are behind a series of attacks against Palestinians and their property.
The Palestinians claim the West Bank, Gaza Strip and east Jerusalem, areas captured by Israel in the 1967 Mideast war, for a future independent state.
But peace talks between Israel and Abbas have remained frozen for more than four years, while divisions between Abbas and his Hamas rivals, who seized Gaza from his forces in 2007, have further hindered peace efforts.
Press; By IBRAHIM BARZAK]
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