The fighter opened fire from the car he was driving and hurled a bomb at security men, slightly injuring four of them, said a ministry statement reported by official media.
"Security forces at the scene chased the car and encircled it, trading fire with the driver, who was killed on the spot," the statement said.
The incident occurred as security forces were combing the scene of Tuesday evening's clash in the Saudi capital in which a suspected fighter and a civilian were killed, the ministry said.
Security forces also arrested "a suspected member of the deviant group" in the Red Sea city of Jedda on Wednesday, the ministry added, using the official term for suspected al-Qaida fighters.
They have killed more than 100 people and wounded hundreds more since launching a wave of bombing and shooting attacks in May 2003.
Many fighters and security men have been killed in clashes since the wave of attacks began. Hundreds of suspects have been rounded up.
The man was wounded "while resisting security forces and attempting to flee," the ministry said, promising to release more details later.
Earlier on Wednesday, the interior ministry said a suspected fighter and a civilian were killed during a shootout between Saudi security forces and armed men in Riyadh on Tuesday evening.
"Security forces chased a car carrying two members of the deviant group," the ministry said.
Saudi policemen also uncovered
weapons and other ammunition
"The car stopped near a gas station inside a residential district of Riyadh. When security forces approached the vehicle, those inside it opened fire," a ministry official said, quoted by the state SPA news agency.
The security forces returned fire, killing one of the men and wounding the other, the official said.
A gas station attendant was also killed, and a security man slightly injured, he said.
Security forces seized automatic weapons, ammunition, bombs, explosives, forged documents and an unspecified amount of money in the car, the official added.
He did not disclose the identity of the two members of the "deviant group."
Fighters stormed the US consulate in Jedda on 6 December, killing five non-American staff members in the latest attack claimed by al-Qaida members.