In a news release, campus officials said it was necessary to place police Chief Annette Spicuzza on leave to restore trust and calm tensions following Friday's crackdown on the "Occupy UC Davis" encampment, which resulted in 10 arrests.
The school has also placed two officers on administrative leave.
Videos posted online clearly show one riot-gear clad officer spraying a line of protesters as they sit passively with their arms intertwined. Spicuzza told the AP that the second officer was identified during an intense review of several videos.
On Sunday, UC President Mark Yudof said he was "appalled" by images of protesters being pepper-sprayed and plans an assessment of law enforcement procedures on all 10 campuses.
"Free speech is part of the DNA of this university, and non-violent protest has long been central to our history," said Yudof, who heads the 10-campus UC system. "It is a value we must protect with vigilance."
Yudof said it was not his intention to "micromanage our campus police forces," but he said all 10 chancellors would convene soon for a discussion "about how to ensure proportional law enforcement response to non-violent protest."
Protesters from Occupy Sacramento planned to travel to nearby Davis on Monday for a noon rally in solidarity with the students, the group said in a statement.
UC Davis officials refused to identify the two officers who were place on administrative leave but one was a veteran of many years on the force and the other "fairly new" to the department, Spicuzza earlier told The Associated Press.
She would not elaborate further because of the pending probe.
"We really wanted to be diligent in our research, and during our viewing of multiple videos we discovered the second officer," Spicuzza said. "This is the right thing to do."
Both officers were trained in the use of pepper spray as department policy dictates, and both had been sprayed with it themselves during training, the chief noted.
David Buscho, a UC Davis senior from San Rafael, said he and his girlfriend were pepper-sprayed Friday.
"I had my arms around my girlfriend. I just kissed her on the forehead and then he sprayed us. Immediately we were blinded," Buscho told The AP. "So I was sitting their blind, suffocating. My girlfriend was writhing in pain. I wanted to touch her but my hands were covered in pepper spray."
"He just sprayed us again and again and we were completely powerless to do anything," Buscho said. "This was my first protest. I've never seen any police brutality in person like that."
Meanwhile, UC Davis Chancellor Linda Katehi said she asked the Yolo County District Attorney's Office to investigate the department's use of force. She said she's been inundated with reaction from alumni, students and faculty and also would speed up an investigation that was to have taken three months.
"I spoke with students this weekend and I feel their outrage," Katehi said in a statement Sunday.
Katehi also set a 30-day deadline for her school's task force investigating the incident to issue its report. The task force, comprised of students, staff and faculty, will be chosen this week. She earlier had set a 90-day timetable. She also plans to meet with demonstrators Monday at their general assembly, said her spokeswoman, Claudia Morain.
The UC Davis faculty association called for Katehi's resignation, saying in a Saturday letter there had been a "gross failure of leadership." Katehi has resisted calls for her to quit.
"I am deeply saddened that this happened on our campus, and as chancellor, I take full responsibility for the incident," Katehi said Sunday. "However, I pledge to take the actions needed to ensure that this does not happen again. I feel very sorry for the harm our students were subjected to and I vow to work tirelessly to make the campus a more welcoming and safe place."
The incident reverberated well beyond the university, with condemnations and defenses of police from elected officials and from the wider public on Facebook and Twitter.
"On its face, this is an outrageous action for police to methodically pepper spray passive demonstrators who were exercising their right to peacefully protest at UC Davis," Senate President Pro Tem Darrell Steinberg, D-Sacramento, said in a statement Sunday. "Chancellor Katehi needs to immediately investigate, publically explain how this could happen and ensure that those responsible are held accountable."
The protest Friday was held in support of the overall Occupy Wall Street movement and in solidarity with protesters at the University of California, Berkeley who were jabbed by police with batons on Nov. 9.
Nine students hit by pepper spray were treated at the scene, two were taken to hospitals and later released, university officials said.
Meanwhile Sunday, police in San Francisco, about 80 miles west of Davis, arrested six anti-Wall Street protesters and cleared about 12 tents erected in front of the Federal Reserve Bank.
Across the bay in Oakland, police cleared out the city's two remaining Occupy encampments on Sunday and Monday. Authorities say protesters at both locations left peacefully and no arrests were made.