The 26-year-old Iranian's left arm was deemed not to be straight on his second 245kg clean and jerk attempt.
Sajjad Anoushiravani, Iran's head coach, said there was a "conspiracy".
Georgia duo Lasha Talakhadze and Irakli Turmanidze won gold and bronze, while Armenia's Gor Minasyan took silver.
Defending champion Salimikordasiabi, nicknamed 'Salimi', and his team approached the five-member jury - an action which is against the rules - and remonstrated with the officials for several minutes as the competition continued.
The jury had overruled two of the three judges, who approved the attempt.
"There's a conspiracy. Our enemies were on the jury," said Anoushiravani, appearing to be referring to a jury member from Iraq.
"It's obvious they took the medal from Salimi. The jury was selected for this to happen."
Salimikordasiabi also failed to straighten his left arm sufficiently with his first effort and was never close with his third after setting a 216kg world record in the snatch earlier.
Iranian supporters in the crowd booed Talakhadze, who claimed the gold with a world record 473kg total.
"It was getting ugly and we asked the competition manager to call security because of the behaviour by the Iranian officials," said Sam Coffa, chairman of the International Weightlifting Federation (IWF) technical committee.
The IWF website was unavailable after it was hacked on Wednesday by someone who plastered the homepage with Salimikordasiabi's name and photograph.
The IWF's Instagram page was also flooded with over 285,000 comments after the incident with one user writing: "Behdad is winner in our hearts. God damn the Olympics."
Iranian state television said the decision was "unfair" and a video of Salimikordasiabi crying went viral.
The Iran team face sanctions for their behaviour.
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Security forces were called to the Olympic weightlifting arena after Iranian coaches reacted furiously when a lift by Behdad Salimikordasiabi in the +105kg category was ruled invalid.