Hirvonen's Citroen DS3 WRC was found to contravene technical regulations, with the non-conformity of the car's clutch being cited as the reason for exclusion. There is a secondary problem for the factory Citroen team, centred on the turbine wheel in the #2 DS3's turbocharger.
The issue with the turbine wheel is also sufficient for exclusion but this penalty has been suspended pending further investigation. The stewards' decision is due imminently.
Citroen says it will appeal against the decision, with the team's technical chief Xavier Mestelan-Pinon insisting that the parts offered no performance advantage.
"The scrutineers identified differences in between the homologation sheet and two components: the clutch and the turbocharger," he said. "The Citroen DS3 WRC's clutch mechanisms are homologated with lightening holes. Our supplier recently provided us with a batch of parts that were not perforated and one of them was fitted to the #2 DS3 WRC.
"These parts don't provide any gain in terms of performance, as they are heavier than those which are homologated.
"Regarding the turbocharger, which is a standard part on all World Rally Cars, the wheel turbine dimension exceed the maximum authorised. This difference comes from dilatation, as the wheel is subject to extreme temperature and rpm factors."
In addition to giving Ostberg a maiden World Rally Championship win, Hirvonen's exclusion from the Faro-based event elevates Evgeny Novikov to second and gives Petter Solberg a podium finish, and ensures that Sebastien Loeb retains the points lead - which he had looked set to lose to his team-mate.
The Finn had ended up dominating a difficult rally, on a weekend when all the other usual frontrunners made mistakes.
Loeb had crashed out on the opening night on Thursday, and Ford duo Jari-Matti Latvala and Solberg then slid out of the lead on consecutive stage amid torrential rain on Friday.
That left Hirvonen to control the rest of the weekend. His final margin of victory was 1m51.8s over Adapta Ford's Mads Ostberg, as Russian Novikov (M-Sport Ford) secured his maiden WRC podium in third. Both independent Ford drivers survived final day scares - Ostberg's car developing a misfire on Sunday morning, and Novikov driving most of the final loop with a broken throttle pedal.
Despite this issue, Novikov managed to hang on just ahead of Solberg - who surged back up the order under Rally 2 to take fourth, even though a power steering failure cost him more time on Saturday afternoon. Team-mate Latvala had a fuel pressure problem on leg three and lost 12 more minutes on top of his Friday crash delay, and had to settle for 14th place and two power stage bonus points.
Nasser Al-Attiyah recovered from a late puncture on his Qatar Citroen to win a close fight for fifth with Czech National Ford driver Martin Prokop, as both celebrated career-best WRC finishes.
Dennis Kuipers took seventh on his first appearance of 2012 in an M-Sport Ford, despite Sebastien Ogier's best efforts to catch him in the giant-killing Volkswagen-entered S2000 Skoda.
Thierry Neuville was in the top five for Citroen Junior until his car overheated on Friday morning. The Belgian recovered to ninth - although he must get back to service on a damaged tyre to secure the result after two punctures on the final loop.
Jari Ketomaa scored a point in 10th at the end of an issue packed weekend in the Autotek Ford, taking the place on the last stage when Peter van Merksteijn Jr's private Citroen broke a driveshaft.
None of the Minis made it into the top 10. Local hero Armindo Araujo's weekend went awry early when he crashed on Thursday night, and Prodrive's Patrik Sandell lost fourth place to damaged suspension on Saturday afternoon. Sandell's team-mate Dani Sordo took a number of stage wins as he flew under Rally 2 following Thursday evening electrical issues, although a later exhaust problem and punctures limited him to 12th at the finish. Sordo did at least get three points for winning the power stage.