The hoax report centred on the same area of the occupied West Bank where three Israeli teenagers were kidnapped and murdered less than a year ago.
It sent hundreds of soldiers, police and agents of the Shin Bet security agency hammering on the doors of frightened Palestinian villagers as they searched house-to-house in the hills around Hebron.
A hearing in Jerusalem magistrates court found that one of the men, 22-year-old Niv Asraf, had concocted his own disappearance to try to win back his ex-girlfriend.
"He said he was seeking attention," Brigadier General Moti Almoz, the chief military spokesman, told Israel's Channel Two television.
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Media reports said the plan was that after going missing Asraf would reappear in a few days, claiming to have made a daring escape from his captors.
What police said turned into a million-shekel (240,000-euro) manhunt started yesterday afternoon.
Asraf's friend, Eran Nagauker, told investigators that the two had been travelling together when a tyre on their vehicle blew out near the Palestinian village of Beit Anun.
The village became the focal point of the Israeli search, with troops flooding into the area to search homes and fields and set up roadblocks, an AFP journalist at the scene said.
The Jerusalem Post said that suspicions about the report of a kidnapping were aroused early on when security forces arriving at the car found nothing wrong with the tyres.
Asraf was tracked down at around midnight camped out in a dry river bed in the sprawling Jewish settlement of Kiryat Arba, next to Hebron, police and the military said.
"Took me 10 seconds to go from relief to anger following this prank kidnapping," army spokesman Lieutenant Colonel Peter Lerner wrote on his official Twitter account.
Both men are accused of giving false evidence, breach of public order and obstructing a police officer in the performance of his duty.
The June 2014 killings of three teenagers in the Hebron area triggered a series of events that led to the devastating 50-day war in the Gaza Strip.