Iran's Ali Mazaheri cried foul when the heavyweight was disqualified after being warned three times for persistent holding against Cuban Jose Larduet Gomez despite leading by two points going into the second round.
"It was a fix. I could have got a bronze easily if it hadn't been for that," an irate Mazaheri, who walked out of the ring before the decision was officially announced, said.
"In my previous fights I had done really well. It was a set up."
The International Amateur Boxing Association responded to Mazaheri's allegations in an email to Reuters, saying: "The Iranian boxer received three warnings during his bout.
"According to Rule 12.2.1 of the AIBA Technical & Competition Rules, 'only three warnings may be given to the same boxer in one contest. The third warning brings automatic disqualification'."
Two bouts earlier, Japan's bantamweight Satoshi Shimizu, trailing by seven points going into the last round against Magomed Abdulhamidov, knocked the Azerbaijani down six times, the first of which he struggled to get up from.
The judges scored the round 10-10, handing Shimizu two extra points for a warning against Abdulhamidov, who propped himself up against the top rope as the referee raised his hand in victory.
The 25-year-old fighter was helped out of the ring by his trainer and Shimizu's team appealed the outcome.
The Japanese boxer's team leader Masamori Yamane accused the referee of trying to support Abdulhamidov by attempting to fix his headgear.
After deliberating for over an hour, AIBA said that under its rules, the referee should have given the Azerbaijani fighter "at least" three standing counts which would have resulted in the contest being stopped.
They, therefore, overturned the result, handing victory to Shimizu, who was staggered by the original decision hours earlier.
"I was shocked about the result. He fell down so many times.
Why didn't I win? I don't understand," Shimizu said, adding he thought the referee should have stopped the fight with Abdulhamidov obviously groggy in the final round.
"This is the second Olympics I have attended and even in Beijing I wasn't happy about the judgement, so I don't know what to do about that. I am really not happy about that."
AIBA officials will consider on Thursday whether to sanction the referee in Shimizu's bout, the association said in a statement.
In December last year, an AIBA-appointed investigation committee dismissed allegations that Azerbaijan was promised two boxing gold medals the London Olympics in exchange for a $10-million loan to the sport's ruling body.
In a statement released at the time, the Special Investigation Committee (SIC) said the report aired on September 23 on the BBC's Newsnight programme was "groundless and unsupported by any credible evidence".
Before sitting down to commentate on the session for British radio, former world heavyweight champion Lewis said he was impressed by the talent on show but had concerns about the judging.
"What I'm concerned about is probably the judging. You never know who is going to win until the end of the fight," said Britain's Lewis, a dual citizen who won gold for Canada in 1988.
Another fight that split opinion on the night was the super heavyweight last 16 bout between Britain's Anthony Joshua and Cuba's Erislandy Savon.
The judges scored it 17-16 in the Briton's favour to cap a successful day in the ring for the host nation after Luke Campbell had earlier beaten Vittorio Parrinello of Italy 11-9 in his bantamweight last 16 fight.
Ireland's John Joe Nevin also moved into the last eight in the bantamweight division after a 15-10 win over Kanat Abutalipov of Kazakhstan.