Morbidelli, who qualified second, won the Teruel Grand Prix following Nakagami's first-lap crash from pole.
The Italian was never seriously challenged and moved to within 25 points of season leader Joan Mir with his second victory of the year, now fourth in the standings.
Morbidelli reflected: "It was a beautiful race. I knew I had to do an aggressive race, and when I saw that I had space and a clear track, I told myself to give my best lap after lap.
"The concentration was at the maximum, the feeling was excellent and everything came easy for me.
"It was a phenomenal race. I was always consistent. This was the best of my career."
Explaining his tactics after Nakagami ran wide and skidded off the track, he added: "After Nakagami's crash, at the start, I told myself that I had to give everything.
"I was convinced of our work, I believed a lot in our bike and in the durability of the tires.
"I pushed hard until the end, when it seemed to me that I was in difficulty but the others were too.
"It is a team victory, which came from the great work of everyone, from [crew chief] Ramon Forcada to the others who put their heart into it.
"In the race, I think I entered a sort of bubble, a magical area, where everything came naturally to me. It was a race that slipped away like a glass of water."