Taekwondo officials want Matos and his coach banned for life from the sport. But Castro expressed "our total solidarity" for both Matos and his coach Leudis Gonzalez.
Matos was winning 3-2 in the second round when he fell to the mat after being hit by his opponent, Kazakhstan's Arman Chilmanov, and was disqualified for taking more than his one minute of injury time.
Matos angrily questioned the call, pushed a judge and then pushed and kicked referee Chakir Chelbat of Sweden, who needed stiches to repair his lip. Matos then spat on the floor and was escorted out.
Taekwondo officials called Matos' behavior an insult to the Olympic vision. Matos' coach countered that the match was fixed and accused the Kazakhs of offering him money.
Castro said the alleged bribery attempt gave Matos good reason to expect the judges to treat him unfairly.
"They had tried to buy his own coach," Castro wrote in his essay published in state media. "He could not contain himself."
Cuba is accustomed to winning golds in boxing, but settled this year for four silver and four bronze medals. Overall, Cuba took home only two golds, down from nine in Athens four years ago.
"I saw when the judges blatantly stole fights from two Cuban boxers in the semifinals," Castro wrote. "Our fighters ... had hopes of winning, despite the judges, but it was useless. They were condemned beforehand."
The ailing, 82-year-old ex-president also noted that defections have taken their toll, blaming "the repugnant mercenary actions" of promoters who lure Cuban boxers off the island with lucrative contracts.
And Castro hinted that big changes could be in order for Cuban sports, pledging a serious review of "every discipline, every human and material resource that we dedicate to sport."
"Cuba has never bought an athlete or judge," Castro wrote, adding that Cubans need to begin preparing now for London in 2012. "There will be European chauvinism, judge corruption, buying of brawn and brains ... and a strong dose of racism," he predicted.