Tuesday's blast, which also left 13 soldiers wounded, struck near an area of no man's land where thousands of Syrian refugees are stranded and where the frontiers of Iraq, Syria and Jordan meet.
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Quoting an unnamed source, the Amaq statement said the attack against "the Jordanian-American base at Rukban in Jordan was carried out by an Islamic State fighter".
According to the Jordanian army, the suicide bomber set off from the makeshift Syrian refugee camp near the Rukban crossing in Jordan's remote northeast.
He then entered Jordanian territory through an opening used for humanitarian aid deliveries and blew himself up as he reached a military post, it added.
Jordan hosts hundreds of thousands of Syrian refugees and thousands more have been stranded at the frontier since January.
King Abdullah strongly condemned the attack and said that Jordanian armed forces would strike back "with an iron fist".
Soon after, the army issued a statement declaring Jordan's desert regions that stretch northeast to Syria and east to Iraq "closed military zones".
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Jordan is part of the US-led coalition fighting IS in Syria and Iraq and while attacks on its territory are rare, it has been targeted by jihadists before.
Tuesday's bombing came two weeks after a gunman killed five Jordanian intelligence officers in a Palestinian refugee camp north of the capital.
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