It was the first air strike on Gaza in more than two months and came shortly after two rockets were fired towards southern Israel.
Despite the flareup along the Gaza border, which has been quiet for months, Israeli officials said it was unlikely to affect the prisoner release which is due to take place on Tuesday night as part of the ongoing direct peace talks with the Palestinians.
Witnesses said the air strike targeted a training ground west of Beit Lahiya which was used by militants from the armed wing of Gaza's ruling Hamas movement.
Neither the air strike nor the earlier rocket attacks on southern Israel caused any damage or casualties.
The Israeli military confirmed the strike, saying the air force had struck "two concealed rocket launchers" in northern Gaza following an earlier cross-border attack.
"This targeted strike ... is an immediate response to the terrorist aggression and its infrastructure in Gaza. Hamas must take responsibility for these actions or pay the price for inaction," said a statement issued by Lieutenant Colonel Peter Lerner, a military spokesman.
Earlier on Monday, militants fired two rockets at the southern Israeli port city of Ashkelon, one of which was shot down by the Iron Dome missile defence system, the army said.
And on Sunday, a mortar shell was fired over the border that also caused no damage or injuries. In September, there were two instances of rocket fire, but Israel did not respond.
It was the first Israeli air strike since August 14 when the air force hit targets in the same area, also in response to rocket fire.
That attack occurred just hours after Israel released a first batch of 26 Palestinian prisoners in line with commitments which led to a resumption of direct peace talks in late July, following months of sustained US pressure.
But Monday's scuffle along the Gaza border was not expected to have any impact on plans to free a second batch of prisoners, with a senior official telling AFP it "won't delay" the release of 26 long-term inmates.
The list of prisoners slated for release, 21 of them from the West Bank and five from Gaza, was approved on Monday by senior Israeli ministers.
The names were published later that night, giving victims' families and groups 48 hours to mount a legal challenge before the release goes ahead.
All but one of them were arrested before the signing of the 1993 Oslo peace accords, which won the Palestinians limited self-rule but failed to bring about an independent state.
Israeli Prime Minister Benjamin Netanyahu pledged to release a total of 104 Palestinians in four stages in line with commitments which brought about a resumption of direct talks on July 30 after a hiatus of nearly three years.
Last week, an Israeli official said that in parallel with the release, a new batch of tenders would be announced for construction in settlements in the West Bank and annexed east Jerusalem, in a move allegedly coordinated in advance with the US and the Palestinians.
The Palestinians have denied any such link.
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