Ricciardo initially finished second to Mercedes driver Nico Rosberg to become the first homegrown driver to take to the podium in the 29-year history of the Australian GP.
The celebrations did not last long as F1 stewards said his car breached fuel-flow rules introduced this year which limit cars to 100 kilograms of fuel during the race. World motorsport governing body FIA subsequently disqualified Ricciardo , elevating McLaren drivers Kevin Magnussen and Jenson Button to second and third.
Red Bull immediately announced it will appeal.
Shortly after the end of the race, FIA Formula One technical delegate Jo Bauer said Ricciardo's car had "exceeded consistently the maximum allowed fuel flow" and referred the matter to stewards.
More than three and a half hours later, after Ricciardo had left the track, the stewards disqualified the Australian saying Red Bull had not only breached technical regulations by exceeding the allowed fuel flow, but also had disregarded instructions before the race to change the fuel flow sensor and during the race to reduce the flow.
The operation of the fuel-flow sensors had been a source of dispute between the teams and the FIA coming into the first race.
After the findings, Red Bull said "Inconsistencies with the FIA fuel flow meter have been prevalent all weekend up and down the pit lane. The team and (engine-maker) Renault are confident the fuel supplied to the engine is in full compliance with the regulations."
Horner further proclaimed the team's innocence to reporters saying; "It is no fault of Daniel. I don't believe it is the fault of the team."
"I am extremely disappointed, quite surprised ... hopefully through the appeal process it will be quite clear that the car has conformed at all times to the regulations," he added. "We would not be appealing unless we were extremely confident that we have a defendable case."
The Albert Park crowd earlier offered Ricciardo a thunderous applause as the stood on the podium in his first race with Red Bull.
"It's a bit overwhelming for now, but just an unbelievable day," the 24-year-old said shortly after.
Australia staged its first Grand Prix of the F1 era in Adelaide in 1985, with the 1986 edition marking the final race of Australian world championship winner Alan Jones.
Mark Webber's first F1 race was the 2002 Australian GP, and since then Australian fans have waited impatiently for a top-three finish at Albert Park.
Red Bull, last year's constructor's champions and a dominant force in F1 for the past four years, had a difficult time in preseason testing and little was expected from its first race of the season.