In a complex ruling, Ricciardo's car was excluded after the team rejected the accuracy of an FIA sensor and relied on its own measurements to comply with the rule governing the maximum allowed flow of fuel into the engine.
"We wouldn't be appealing if we weren't extremely confident we have a defendable case," said team boss Horner.
Stoddart, who sold his Minardi team to Toro Rosso owners Red Bull in 2005, tipped Red Bull to prove to the FIA that it didn't cheat.
"The Renault engineers would've known exactly how much fuel was going into that engine," the Australian told Melbourne radio 3AW on Monday.
"We're talking teams with budgets of $400, $500 million here -- they have far better equipment than the FIA."
The correspondent for the London newspaper The Times, Kevin Eason, wrote: "In the other corner (to Red Bull) is the FIA, essentially an amateur organisation with a budget a fraction of the F1 teams."
Stoddart tipped Red Bull to be able to prove that Ricciardo "did not gain any advantage" and that it decided to ignore the FIA because it was the "right" thing to do in the circumstances.
Horner explained: "We could see a significant discrepancy with what the sensor was reading and what our fuel flow was stated as.
"These (FIA) fuel flow sensors have proved problematic. So we relied on our own data, because otherwise we would have lost a lot of engine power," he is quoted by Speed Week.
The FIA's Charlie Whiting, however, said he advised Red Bull repeatedly throughout the race weekend to "take the necessary steps" to comply with the rules.
"If they had followed the advice we gave them at the time, we would not have had a problem and they would not have been penalised," he said.
"If their sensor was kaput, then things would have been different," Whiting added. "It is a human thing because they have the ability to do what was needed to comply."
Red Bull's case is further weakened by the words of Mercedes engine boss Andy Cowell, who said the way the fuel flow is measured is "accurate and reliable".
"All the teams have their own consumption measurements via the injection data," he is quoted by the German-language Spox.
"In the case of irregularities, the FIA will compare its values with those of the team. So we have a safety net."