While Tech 3 KTM rider Miguel Oliveira romped to a fairytale victory from pole on home soil at Portimao on Sunday, Morbidelli sat in the runner-up spot until the final lap, when Miller passed him at the Turn 13 hairpin and fended him off around the final few corners.
But third place was still good enough for the Italian to maintain his hold on second in the championship ahead of Suzuki’s Alex Rins, who finished down in 15th.
Rins’ teammate Joan Mir had already wrapped up the title last time out at Valencia.
“I’m more happy about the second place in the championship than the place lost on the last lap,” Morbidelli said. “Jack was very good, very strong, especially at the end, he was stronger than me, he was clever.
“He was able to overtake me and he didn’t give me the chance to retaliate. So huge congratulations to him and also Miguel, who was untouchable today.
“I tried it in the beginning just to see if I was able to stay close to him, but I wasn’t. I realised in the beginning quite soon that I wasn’t able to stay with him.
“Then I tried to just push at 200 percent, tried to risk a lot anyway because I wanted to make a podium finish in the last race of the championship and finally we did it.”
The battle for second in the standings
Morbidelli’s third season in the premier class yielded three victories – equal to teammate Fabio Quartararo’s haul – and a further two podium, as well as two pole positions.
Looking ahead to next year, when he will partner mentor Valentino Rossi at Petronas, Morbidelli says he now has more “self-trust” in his abilities and will have higher expectations.
“I will have more knowledge about myself,” he added. “I will have more self-trust and I will have more expectations because we know what we can do and we know what we can do when things are at its place.
“For sure next year is going to be an important year for us and it’s going to be an interesting year, but after all we are satellite riders, I will be a satellite rider. I will have expectations, but not too much because I will anyway [still] be a satellite rider.”