As many as 143 people were injured when the bomber blew himself up in a packed dining room at the Park Hotel on the eve of the Jewish Passover holiday.
Chance find
Israel responded by launching a large military campaign, retaking control of West Bank cities from the Palestinian Authority.
Omar Jabar had been sought by Israel ever since the attack.
Palestinian sources said he was arrested together with deputy Hani Barabra in the village of Bala, AFP news agency reported.
Israeli military sources said he had been found by chance during a separate operation.
In 2005, an Israeli court convicted another Hamas leader, Abbas Sayad, of masterminding the Netanya bombing.
Two years earlier, four Palestinians were sentenced to life imprisonment for their role in the attack.
They and the bomber, Abdel Basset Odeh, were all members of Hamas, which claimed responsibility for the bombing.