Security forces and media reports said the men died during an armed clash in a suburb of the Saudi capital Riyadh.
"The clashes are over. The (suspects') lair was assaulted and we killed those we found there," said a security source, according to AFP.
Earlier, police had surrounded the hideout in the Al-Yarmuk suburb, and there were reports of automatic gunfire and grenades.
The Dubai-based Al-Arabiya television channel reported that "all the suspects, who were barricaded in a house in the east of Riyadh, have been killed," putting the toll at five.
According to its correspondent a large quantity of arms were seized from their hideout which had earlier been besieged by security forces amid a fierce firefight with automatic arms fire and grenades.
The names of the five dead men were on a Saudi most-wanted list of 36 people, the TV network said.
It has also been reported that forces seized a large quantity of arms from the hideout.
The men were said to have been linked to the oil refinery plot, an attempted suicide bomb attack on the world's largest oil-processing plant at Abqaiq, in eastern Saudi Arabia, last Friday.
The attack was thwarted, leaving two security men and the two would-be bombers dead.
An al-Qaeda statement posted on the Internet claimed responsibility for the attack and identified the two "martyrdom-seekers".
The terrorist network vowed to attack more Saudi oil installations.
The firing began at around 5am GMT) after a large number of security personnel were deployed in the area, a resident said.
"The clashes began when the security forces were deployed around the terrorists' hideout" the source said.
The two suicide-bombers involved in the refinery attack both appeared on a list of suspected al-Qaeda members sought by Saudi Arabia, the interior ministry said on Sunday.