Sydney - Sonny Bill Williams and Francois Botha agreed to a ten-round fight before they met in Brisbane on Friday.
Williams has said on his Twitter account both boxers knew the heavyweight bout would be over ten rounds; not twelve.
And Botha’s promoter, Tinus Strydom, told local media he had reluctantly agreed to the change shortly before the fight, which Williams won on points.
GALLERY: Sonny Bill Williams v Francois BothaVIDEO: Sonny Bill Williams v Francois Botha - highlights
The 27-year-old rugby international was in trouble at the end of the tenth round of his sixth professional fight as the 44-year-old Botha came within seconds of knocking out the New Zealander.
Controversy erupted after the result was announced because just about everyone believed the fight had to be over 12 rounds because it was for the WBA international title.
Botha still described the result as "match-fixing" and spectators and bookmakers were enraged.
An Australian boxing official told local pay TV channel Fox Sports on Saturday both camps had agreed to shorten the bout.
The fight's status as a title bout was plunged into doubt, however, with confirmation that no WBA official was present.
"Whether the fight was formally sanctioned by the WBA, you'd have to ask the WBA or the promoter. We don't get involved in the sanctioning," John Hogg, a committee member of the Australian National Boxing Federation, told Fox Sports.
Hogg's comments contrasted with the confusion expressed by the Federation’s vice-president, Alan Moore, who was one of the judges. He told The Australian newspaper he had "no idea" the bout would be shortened.
"When the ring announcer said that it was the last round, that was the first we (the judges) knew of any change," Moore was quoted as saying.
The controversy has come at a sensitive time for sport in Australia, where police are investigating at least one potential case of match-fixing, and an explosive report warning that local competitions were at a high risk of manipulation by organised crime.
The abbreviated fight was slammed by bookmaker TAB New Zealand, who refunded "pick the round" bets on the fight.
"We went to great pains to double check and triple check that it was 12 rounds because (in) a Sonny Bill fight this has happened before," TAB New Zealand bookmaker Mark Stafford, whose agency refunded 'pick-the-round' bets, told New Zealand radio on Saturday.
"So we're pretty annoyed about it."
Stafford said his agency had taken bets on three of Williams's six professional fights, with two of them shortened without anybody knowing. He added that they were doubtful about opening another book with the rugby player.
Bookmaker Sportingbet Australia said it would refund all bets laid on Botha.
Disgruntled fans took to social media pages to slam the bout as a sham, and demanded broadcasters refund the pay-per-view fees for the fight.
"If you work an 8-hour day tomorrow, work just six. If the boss asks you why, say it’s the SBW clause," one Twitter user said in a post.
Strydom said he would lodge a protest with the WBA. But Williams's manager, Khoder Nasser, said the South African camp's complaints were sour grapes.
"They're going to look for any excuse because they lost," Australian state broadcaster ABC quoted him as saying on its website.
"If there's a misunderstanding, there's a misunderstanding and I'm sure we'll deal with that with the WBA."
Williams, set to re-start his rugby league career in Australia after several years of playing rugby union, including a World Cup win with the All Blacks in 2011, had a clause in his New Zealand Rugby Union contract allowing him a set number of fights to pursue his boxing career.
But his six professional victories, coming against a string of ageing or unfit journeymen, have been slammed by established fighters and pundits as commercial ventures lacking credibility.