He was freed on parole in Pretoria last week and immediately flew back to Bangkok, government officials told AFP.
Chumlong Lemtongthai pleaded guilty in 2012 to running bogus rhino hunts as a cover to source horns to sell on the lucrative black market.
His long sentence had been hailed by campaigners as a breakthrough in the criminal prosecution of traffickers. But his release triggered accusations that South African authorities were failing to act to stop the slaughter.
"His early release is an utter disgrace. It makes a complete mockery of the seriousness of the crimes perpetrated," Audrey Delsink, director the Humane Society International animal charity, told AFP.
"It sends a strong message that high-level poachers with known links to wildlife trafficking networks are treated with leniency.
"Lemtongthai was personally involved in the illegal slaughtering of 26 rhinos, and ordering the deaths of at least 50 animals."
The World Wildlife Fund said authorities must push for "successful prosecutions and appropriate sentencing of those responsible".
Lemtongthai enlisted Thai prostitutes to pose as fake hunters on game farms in North West province, obtaining permits from the provincial authorities to shoot a set number of rhino.
Professional hunters shot the rhino and Lemtongthai's Laos-based trafficking network used false paperwork to traffic the horns as legitimate hunting trophies before selling them on Asia's traditional medicine market.
Driven by rocketing demand in Asia, the number of rhinos killed in South Africa has climbed steeply in the past decade from just 13 in 2007 to reach more than 1,000 annually in the past five years.
In the last eight years alone, roughly a quarter of the world population of rhinos has been killed in South Africa, home to 80 per cent of the remaining animals.
Rhino horn is composed mainly of keratin, the same substance as in human nails, and is falsely believed by some to have powerful healing properties.
"Unfortunately, people connected with him will be back, or are back already, and the slaughter will continue," forensic investigator Paul O'Sullivan told the Oxpecker wildlife investigative group that tracked the case.
Lemtongthai's 40-year sentence was reduced on appeal in 2013 and again in 2014.
"When the parole board considered his profile, they saw fit that he was ready for parole. We applied law as prescribed," correctional services department spokesman Singabakho Nxumalo told AFP.
"We don't expect him back in the country."