The Frenchman had reduced his team-mate’s lead from 40 minutes to just over two minutes in recent stages and appeared to have the momentum going into the longest stage from Antofagasta to El Salvador in Chile.
But Mini boss Sven Quandt’s decision to enforce team orders crushed Peterhansel’s shot at a 12th Dakar title and left any hopes of a thrilling climax in tatters.
Orlando Terranova of Argentina claimed a low-key stage victory, 11 minutes ahead of Roma and 14 clear of Peterhansel.
“The game is over. We've had a good laugh and enjoyed ourselves,” said Peterhansel.
"The team asked us to not take any more risks. It's a bit frustrating because we've done most of the hard work. But, if Mini wants to have three cars on the podium, at the speed at which we are driving out in front, it's easy to crash a car or even two in just one day.
"We know that this can happen, but I didn't think that they would do it.”
Leader Roma added: "It's disappointing for Stephane [Peterhansel], it's disrespectful. It's a bad decision that has been taken."
Peterhansel is now over five minutes behind Roma in the overall standings, with fellow Mini driver Nasser Al-Attiyah 56 minutes adrift in third.
Race organisers also waded into the debate, expressing their disappointment at the decision to deploy team orders.
"We haven't been informed of this decision by the team manager of Mini," said race director Etienne Lavigne.
"But we are disappointed, clearly, because it is not in the spirit of the competition. It's a little shocking. It's not fair.
"If I was being mean, I would say to Mini that they can collect the trophy immediately. Fighting without risk is triumph without glory."