Williams was clearly in trouble at the end of the WBA international heavyweight title bout against the veteran South African but held on to defy a flurry of punches and win the fight on points.
There was much confusion, however, when the bout, scheduled for 12 rounds, was ended after 10. Botha said his trainer had been told only at the end of the ninth round that the 10th would be the final round.
"It's a championship fight, how can you bend the rules just because he's a superstar rugby player?" said the 44-year-old, who fought Evander Holyfield, Lennox Lewis and Mike Tyson earlier in his career.
"It's unheard of," he told Fox Sports News from his dressing room. "What the WBA should do now is immediately order a re-match."
There was no immediate official explanation for the early end to the fight.
A World Cup winner with New Zealand in 2010 and Super Rugby champion with Waikato Chiefs last year, Williams has elected to return to rugby league with the Sydney Roosters this year and was non-committal about his future in boxing.
"I'm not sure, we'll see how we go," the 27-year-old said.
There was no complaint about the result when Australia fly-half Quade Cooper won his maiden boxing bout with a first-round knockout earlier on the same card.
Cooper took a couple of good punches before putting insurance salesman Barry Dunnett on his back with a clean right hook just before the end of the opening round of their cruiserweight contest.
Despite a dispute with the Australian Rugby Union last year, Cooper has remained in the 15-man code and will be hoping to win his place back in the Wallabies side for this year's British and Irish Lions tour.
While Cooper was fighting, his Queensland Reds team-mates were being beaten 20-8 by the Chiefs in a Super Rugby pre-season friendly on the nearby Sunshine Coast.
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