Palacios stood down as a result of a persistent back problem that resulted in a weeks hospitalisation last week, the club said on its website.
Roger De Sa, whose appointment is with immediate effect has 10 years experience as a coach having started his coaching career as a Player Coach at Wits University. Roger won Coach of the Season in his first year as coach of Wits University and in 2010 won the Nedbank Cup.
Irvin Khoza, chairperson of Orlando Pirates said in a statement: "Roger is a team player who has worked in various capacities for our senior and junior national teams including being roped in to the technical team of the Portuguese national team during the 2010 Fifa World Cup.
"I have no doubt that he will find the new challenge at Orlando Pirates a worthwhile enhancement to his career," added Khoza.
"This has to be the right time as I had years ago contacted the chairman for this job to no avail. When I got the chairperson's call I was obviously delighted as I believe I am up to the task at hand," said De Sa. "It's an honour to be here. This kind of opportunity only comes once in a career."
Roger has represented South Africa in three sporting codes – soccer, indoor soccer and basketball in one year.
Augusto Palacios will return to work in the development structures of Orlando Pirates with due consideration to his recovery which is expected to take several months after undergoing major spinal surgery.
Pirates have had an erratic start to the season, failing to score in their last four games, losing two of them 3-0, against SuperSport United and then Moroka Swallows.
Though the club won their first two games of the season uncovincingly, against Bloemfontein Celtic and Golden Arrows.
Palacios took over from Julio Leal who was fired last season. Palacios then guided the team to the Premiership title in what was a treble winning season.