The women, who appeared to be Korean students, were seen tailing the APO streakers as they left Quezon Hall for the one-kilometer run to Palma Hall.
Both wore masks and covered their genitals with a sheet of cartolina with a message promoting equal rights for women.
After posing for photographers, the two entered a waiting car, which then sped off.
"We were surprised by their act. We were not expecting them to be there, we know nothing about that. They just appeared after our members took off from Quezon Hall," said Joselito Caparino, APO media liaison officer.
He said the act was an affront to their tradition.
"We are condemning their act not on gender issues because they are women, they can do run naked if they want to. But the event was supposed to be ours," he said.
Caparino noted that the APO fraternity has never encouraged members of their sorority to join the run. He clarified that the two women were neither part of the organization nor acquainted with any member.
He said they will conduct an investigation into the "intrusion," and identity of the two women.
"The Oblation Run is a form of protest. It is not true that it is part of our initiation," Caparino explained.
For this year, the Oblation Run’s theme, "Merry Christmas ???," put to question the reasons to celebrate the holidays.
Caparino said the three question marks represent the budget cut for the tuition of the so-called "Iskolar ng Bayan," the backpay and cost of living allowance woes of the UP employees; and the implementation of the EVAT.
"These are the struggles of Filipinos. But what is the answer of our government? Political repression," Caparino said. "All of these make the ‘merry’ in Christmas questionable."
Organizers said the number of participants at yesterday’s Oblation Run was the biggest since the tradition started in 1973.
It was the first time that the run took off from the UP administration building, where the Oblation is located.