Preacher Sheikh Aaidh al-Qarni and a Saudi diplomat, Sheikh Turki Assaegh, were both wounded in a shooting as they left a university auditorium in the southern port city of Zamboanga, where the cleric had been giving an address.
Their Filipino police escorts killed the lone assailant, while two other suspects who were seen with the gunman were arrested as they tried to escape, police said.
"The suspect popped up from the crowd, moved in close and shot the victim" as he was boarding his car, said city police spokeswoman Chief Inspector Helen Galvez, adding that the gunman then walked to the other side of the vehicle and shot the Saudi diplomat.
A uniform for engineering students in the Western Mindanao State University, where Qarni was speaking, was found hidden in his backpack, but university officials could not immediately confirm the gunman was enrolled in the institution.
Islamic State militants who control vast swathes of Iraq and Syria had called on "lone wolves" to attack Qarni and several other Saudi clerics whom they accused of apostasy in the latest issue of Dabiq, their monthly online magazine.
At least 12 militants and five soldiers were killed while more than 30,000 people were displaced over several days of fighting, which ended as the army seized the gunmen's main camp over the weekend.
However, Filipino authorities have not linked sympathisers of Islamic State jihadists to yesterday's attack.
He has been flown to Manila for treatment, according to a Saudi government statement.
Saudi media outlets described Qarni as a senior Islamic scholar and he has more than 12 million followers on Twitter.
Last week, the Saudi embassy in Manila asked local police for increased security for its premises, as well as for the Saudi national airline due to an unspecified threat, Philippine foreign affairs spokesman Charles Jose said.
Zamboanga, 800 kilometres south of Manila, is one of the largest cities in the southern Philippines, an area troubled by a decades-long separatist rebellion by the mainly Catholic nation's Muslim minority that has claimed more than 100,000 lives.
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