Despite starting only 16th, Rossi scythed his way through the field early on and was part of a three-bike fight for victory with Andrea Dovizioso and Alex Rins in the second part of the Valencia Grand Prix.
The Yamaha rider passed Rins for second but couldn't keep up with Dovizioso as the race reached its conclusion, and crashed with five laps remaining.
This marked the second consecutive race that Rossi - who ended 2018 winless - crashed from a strong position as he fell while leading at Sepang two weeks earlier.
"Is a s*** emotion. Is very bad," he said after the race. "Unfortunately this year I wasn't able to win but in the last two races I was very close in dry and wet, this remains [true].
"Is a great shame, I am so sorry because we needed this podium, I need this podium but also Yamaha and also the team because is from Sachsenring that we don't achieve."
Rossi said his crash was a result of a mistake, but added that the team doesn't fully understand how the accident occurred and that it looked similar to his Malaysia incident.
"I did a mistake but sincerely also looking the data we don't understand very well what happened. Is true that is very similar to Malaysia so I lose the rear when I open the throttle.
"Looks like that in the last laps we have to keep more attention with the tyre because we have a bit too much degradation.
"I don't expect, I am very sorry but anyway remain a good Sunday, a good race because I was competitive so in the last two races of the season I don't take any result but I was fighting for the victory, this is a great feeling.
"When you fight for the victory, is something very positive."
Additional reporting by Matteo Nugnes