The 17-year-old had a mathematical chance of securing the title heading into Malaysia, his tally of five wins and seven podiums enough to put him second overall, 56 points down on Sandro Cortese.
He didn't appear in the opening practice session at Sepang however, and amid talk of unhappiness with his team confirmed he has quit the outfit three races before the season's end.
Vinales, who did at least travel to Sepang, blamed the team's poor performance and refusal to allow him to leave at the end of the year for his shock early exit.
"We won't take part in the race as the team hasn't complied with the agreement we had," he said.
"Since halfway through the season, [the team] haven't done all they could.
"I'm always giving my best. I wanted to leave the team after those last three races and have a 'clean' break-up, but they wouldn't agree so today I'm heading home.
"It's definitely always better to finish in a good way. I would have raced until the end of the season if they agreed to release me at the end of the year."
Vinales had recently signed a contract extension with Avintia Blusens, but declared he was now far from confident he could achieve him ambition of winning next year's Moto3 title with the team.
"You can sign whatever you want, but when things just get worse and worse, you have to find solutions," he said.
"It's not that much about the support, but I think it's a second division team.
"I have to try and win the championship next year and I don't think I could do it with this team, so that's why I took this decision."
Vinales' shock withdrawal means Cortese will, barring disaster, clinch the inaugural Moto3 crown this weekend.
The 22-year-old German has fewer wins than Vinales (three to Vinales' five) but has missed the podium just twice all season.
After Vinales, his next-nearest challenger is Luis Salom, 61 points in arrears.