The eight-time world champion stopped on Stage 6 after suffering a front left puncture, losing more than two minutes in the process as he and co-driver Benjamin Veillas fitted a spare wheel.
After winning Stage 5, Ogier had been sitting third, only 4.8s adrift of rally leader and Toyota team-mate Elfyn Evans when the puncture occurred.
"It's rough, and we drive Pirelli so, a good combination,” said Ogier when asked what had happened at the end of the stage.
However, to make matters worse, the rough gravel stages came to bite Ogier again on the next test. A second puncture reduced the Toyota driver to limp through before eventually pulling over and down an access road.
Having elected to take only one spare for the afternoon loop, the puncture ended Ogier’s hopes of fighting for a record breaking sixth Portugal win this year.
It also follows the retirement of long-time rival Sebastien Loeb, who damaged his M-Sport Ford Puma's right rear suspension when he clouted a wall on Stage 5.
Ogier wasn't the only driver suffer tyre issues as a spate of problems hit several of the Rally1 field, running Pirelli’s new updated gravel rubber.
Hyundai’s Ott Tanak suffered an almost identical fate as Ogier with the Estonian incurring punctures on Stage 6 and Stage 7.
Tanak dropped from fifth to 10th after losing more than three minutes. Luckily, a decision to carry a second spare will allow the 2019 champion to continue.
Before Tanak’s misfortune, M-Sport’s Adrien Fourmaux was the first of the drivers to hit trouble when his front left came off the rim in Stage 5, when he appeared on course to set the fastest time.
The Frenchman's team-mate Craig Breen was next to encounter a tyre drama after puncturing his front left on Stage 6 that proved particularly rough for the crews to navigate through.
"This stage is completely destroyed I could have got it in about 150 places because there's boulders everywhere. It's a lottery," said Breen.
Gus Greensmith completed a hat-trick of punctures for the M-Sport team when he suffered a left rear failure that dropped him to sixth behind Hyundai’s Dani Sordo.
After a drama-filled afternoon, Toyota’s Elfyn Evans headed into the day’s penultimate stage with a 7.0s lead over Hyundai’s Thierry Neuville, with championship leader Kalle Rovanpera third despite having to clear the road as the first runner.
