Syria said the Jordanian strikes had killed seven people, including three children and a woman.
Jordan regretted civilian casualties, Government Communication Minister Mohammed al-Momani said on Tuesday said in a post on X on Tuesday.
Jordan said on Monday its air force had struck what it described as militant hideouts in southern Syria after determining that the suspects behind last week's church attack were linked to "terrorist groups" operating there.
Senior government security officials said on Monday that Jordanian security forces had arrested two brothers and their brother-in-law after a shootout over the church violence that killed nine people and wounded at least 34 others.
There has been no claim of responsibility by Islamic State.
The Jordanian armed forces said the operation was conducted in co-ordination with Damascus.
Syria's government said the air strikes were carried out without co-ordination with Damascus and that it had launched an investigation into the attacks.
Friday's assault took place during a funeral at a Greek Orthodox church in the village of Hamoud, about 120km southwest of the capital, Amman.
Witnesses said gunmen opened fire for several minutes.
Reuters video footage showed a building pockmarked by the exchange of fire in the village of al-Judayyda, in Karak governorate.
Jordan's Public Security Directorate said in a statement carried by state media that security forces located the suspects while they were hiding in an abandoned house.
They refused to surrender and attacked security forces, who returned fire and arrested all three after wounding them.
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