One of the oldest Christian church buildings in District Six, it survived forced removals and demolitions during apartheid.
Today the church stands as a heritage site.
Jackson said the fire on Wednesday partially damaged the under-croft of the church.
“How this person entered we don’t know, but he allegedly came in and threw a petrol bomb.
"I doubt they understood or knew the historic significance of this church in District Six.
"This church has served this community for 130 years and been through the darkest days of apartheid when its residential community was obliterated,” said Jackson.
The student was caught on campus by security with another petrol bomb in his hand, Jackson said.
There were others with him but they escaped.
Lukhanyo Matinisi, 20, was arrested.
Police spokesperson FC van Wyk said: “On their arrival, a 20-year-old suspect was handed over to police officer by security personnel who caught him with a petrol bomb in his possession.
"The suspect appeared in the Cape Town Magistrate's Court (on Thursday) on a charge of arson,” said Van Wyk.
In a statement, the Anglican Diocese of Cape Town condemned the criminal activity.
The Archbishop of Cape Town, Rev Thabo Makgoba, chairing meetings of the wider church in Benoni, and Bishop Garth Counsell of Table Bay, expressed their prayers and support on behalf of the Anglican Church of Southern Africa to the people of St Mark’s District Six.
CPUT student and parishioner Mluleki Mzutwa said that life had seemingly returned to normal on campus after the fire and believed the university should provide an introduction of the history of St Mark’s when taking in new students.
Another student, requesting her name be withheld, said that many students knew little of the church or its significance, while others had barely registered the arson attack of the previous day.
CPUT acting vice-chancellor Chris Nhlapo said: “St Mark’s has survived one of the most tragic blights on this country’s history - the forced removals in District Six well over 50 years ago.
"Over the years many staff and students have found refuge there as they were separated from family and friends while pursuing an education.
"More recently the church elders have been integral in our efforts to build a relationship with the District Six community.”