Fernando Alonso was stripped of pole position and moved five places down the Hungarian Grand Prix grid after impeding Lewis Hamilton in qualifying.
Alonso (right) will start from sixth place after his penalty
Hamilton was awarded top slot after being impeded by his McLaren team-mate in the pit lane, leaving him too little time to start his final lap.
McLaren will now not be allowed to score constructors' points.
Renault's Giancarlo Fisichella was also demoted five places to 13th for impeding Spyker's Sakon Yamamoto.
Fisichella's demotion leaves the reigning world champions without a car in the top half of the field for Sunday's race, while Japan's Yamamoto remains at the back.
McLaren have said they intend to appeal against the decision to prevent them scoring constructors' points.
As a result of Alonso's punishment, BMW Sauber driver Nick Heidfeld was bumped up to second place with Kimi Raikkonen third.
Ferrari's Felipe Massa, third in the championship and 11 points adrift of Hamilton, suffered a costly mix-up on his fuel levels and will start from 14th on the grid.
The attitude of the team at the end of qualification was considered prejudicial to the interests of competition and motor racing
Hamilton leads Spaniard Alonso by two points with seven races remaining.
The 22-year-old British rookie was fastest until the Spaniard pipped him by 0.107 seconds with his final lap of the session in the dying seconds.
Hamilton was unable to reply after being forced to wait behind Alonso at their final stop, leaving him too little time for a final flying lap.
Alonso and Hamilton, as well as team principal Ron Dennis, were summoned to an FIA inquiry to explain why the Spaniard had stopped for such a long time.
"The commissioners decided that Alonso unnecessarily interfered with another competitor, Hamilton, and he has been penalised five places on the grid," said an FIA statement.
"The attitude of the team at the end of qualification was considered prejudicial to the interests of competition and motor racing."
McLaren immediately appealed against the decision but this will only cover the withdrawal of constructors' points, not the personal penalty handed out to Alonso.
Hamilton refused to be drawn into criticising Alonso for delaying his exit out of the pit lane ahead of his final run.
"There's not really much to say - you saw what happened," he said.
"The team did a great job and we had very good pace, but I'm not aware of what happened. You should ask the team."
When asked as to how long he missed out on setting a final quick lap, he tersely replied: "About the same amount of time I was held up in the pit stop."
Explaining the incident, Alonso said: "The team was holding me back. We tried to have a little bit of space with the Ferrari (Raikkonen) in front of us."
The delay in Alonso leaving his pit is said to have been caused by an argument between the Spaniard and his engineer about the type of tyres that had been fitted to his car.
McLaren released a statement on Sunday responding to the penalty. It seemed to lay the blame for delaying Hamilton on Alonso, and complained at the unfairness of being denied constructors' points.
"The process of managing two such exceptional talents as Fernando and Lewis is made more challenging by having a race winning car," the statement read.
"Every effort was made [in qualifying] by the team to maintain our policy of equality; however in the heat of the battle there are occasions when the competitive nature of drivers sees them deviate from the agreed procedures.
We do not believe that the findings of the stewards and the severe penalty imposed on the team are appropriate
"During this intense and frenetic period of qualifying, decisions are necessarily made in seconds to enable the drivers and the team to position their cars on the track at the optimal moment.
"We agree with the stewards that, when the team decided to hold Fernando for 20 seconds, there were four cars on the circuit.
"However, we do not understand the relevance of this observation as the team needed to estimate where all the remaining cars would be in the final minutes of the session.
"Similarly the team does not agree with the statement of the stewards that the 20-second hold caused Lewis to be impeded.
"Tensions were undeniably high and the problem at Fernando's first stop, the desire to enter a clear track and concerns expressed following the fitting of used tyres undoubtedly contributed to the delay in Fernando's ultimate departure.
"We do not believe that the findings of the stewards and the severe penalty imposed on the team are appropriate, and that our strenuous efforts to maintain the spirit of fair play and equality within the team have been misunderstood."
Briton Jenson Button, who took a first Grand Prix win from 14th place in a wet race in Hungary last year, qualified his Honda a disappointing 17th.
Results from qualifying, Hungarian Grand Prix
1. Fernando Alonso* (Spa) McLaren -Mercedes 1min 19.674secs
2. Lewis Hamilton (GB) McLaren-Mercedes 1:19.781
3. Nick Heidfeld (Ger) BMW Sauber 1:20.259
4. Kimi Raikkonen (Fin) Ferrari 1:20.410
5. Nico Rosberg (Ger) Williams-Toyota 1:20.632
6. Ralf Schumacher (Ger) Toyota 1:20.714
7. Robert Kubica (Pol) BMW Sauber 1:20.876
8. Giancarlo Fisichella* (Ita) Renault 1:21.079
9. Jarno Trulli (Ita) Toyota 1:21.206
10. Mark Webber (Aut) Red Bull-Renault 1:21.256
11. David Coulthard (GB) Red Bull-Renault 1:20.718
12. Heikki Kovalainen (Fin) Renault 1:20.779
13. Alexander Wurz (Aut) Williams-Toyota 1:20.865
14. Felipe Massa (Bra) Ferrari 1:21.021
15. Anthony Davidson (GB) Super Aguri-Honda 1:21.127
16. Vitantonio Liuzzi (Ita) Toro Rosso-Ferrari 1:21.993
17. Jenson Button (GB) Honda 1:21.737
18. Rubens Barrichello (Bra) Honda 1:21.877
19. Takuma Sato (Jpn) Super Aguri-Honda 1:22.143
20. Sebastian Vettel (Ger) Toro Rosso-Ferrari 1:22.177
21. Adrian Sutil (Ger) Spyker-Ferrari 1:22.737
22. Sakon Yamamoto (Jpn) Spyker-Ferrari 1:23.774
* Penalised five places for impeding a rival
Revised top 10 after Alonso and Fisichella penalty:
1. Lewis Hamilton (GB) McLaren
2. Nick Heidfeld (Ger) BMW Sauber
3. Kimi Raikkonen (Fin) Ferrari
4. Nico Rosberg (Ger) Williams-Toyota
5. Ralf Schumacher (Ger) Toyota
6. Fernando Alonso (Spa) McLaren
7. Robert Kubica (Pol) BMW Sauber
8. Jarno Trulli (Ita) Toyota
9. Mark Webber (Aust) Red Bull-Renault
10. David Coulthard (GB) Red Bull-Renault