Tabotta insists he was leaving regardless of what happened at the Olympics.
But his departure comes as Cycling Australia continues a wide-ranging review into how they returned from the Olympics with only a silver and a bronze medal.
There were realistic expectations that Australia and other nations would break the British stranglehold on cycling at the Olympics.
Instead, Great Britain dominated the sport for the third-straight Games with six golds.
Tabotta is now on leave and will finish on November 4.
Next year he will move into a new role in elite sport, but for now, Tabotta is not saying what that will be.
Tabotta joined Cycling Australia in 1995 and a decade later he became the national performance manager and technical director.
Once Shayne Bannan left in January 2011 to manage the Orica-BikeExchange team, Tabotta was in sole charge of cycling's high-performance program.
While Australian cycling has won only one Olympic cycling gold medal since the 2004 Olympics, the sport continues to boom.
Cadel Evans won the 2011 Tour de France, Orica-BikeExchange is a successful professional road team and Australia remains one of the top nations in the road, track and BMX disciplines.
In Tabotta's time as high-performance boss, Australian cycling has produced more than 50 world champions.
"Not without our challenges, it's been an honour to witness some of the greatest ever performances by Australians on the world stage," Tabotta said.
"I am proud to have played my role to lead the growth of the high-performance unit, and in supporting Australia's best cycling talent in pursuit of international success."
Cycling Australia chief executive Nick Green said they had already started looking for Tabotta's successor.