An official statement issued by the presidency described the incident as "harrowing" and said Zardari had directed Interior Ministry chief Rehman Malik to conduct an inquiry and immediately submit a report.
"No one should be allowed to take the law into his own hands, no matter what the crime is," Zardari was quoted as saying.
The President directed authorities to "dispense justice according to the law in this case".
The unidentified man, who was a 'malang' or hermit, was detained by police at Channigoth town in Bahawalpur district, 400 km from Lahore, after he was accused of burning pages of the Quran on Tuesday.
A mob of about 2,000 people stormed the police station and took the man away after beating up several policemen. The man was then assaulted and burnt alive in front of a crowd of hundreds, police and witnesses said.
Regional police chief Ahmed Ishaque Jahangir told the media that the man was "insane".
