The announcement officially opens a vacancy alongside French rider Fabio Quartararo (24), with LCR Honda's Spaniard Alex Rins (27) a strong contender according to media reports.
Morbidelli was the championship runner-up to Spaniard Joan Mir (25) in 2020 when he won three grands prix but he has not won a race since then. He starts this weekend's British Grand Prix 11th in the standings, two places behind Quartararo.
Yamaha said the Italian was moving on to "new racing challenges".
"It's a shame that the last two years didn't play out the way we both wanted and hoped for," said Yamaha team boss Lin Jarvis.
"We discussed the possibilities to continue our partnership, but ultimately we decided that 2024 would be a moment to make a change, both for Yamaha and for Franky."
Rins, a six times MotoGP race winner including in Texas this season, is currently recovering from surgery after breaking his right leg in a sprint race in Italy in June and has missed the last three grands prix.
He joins from LCR Honda as team mate to French rider and 2021 world champion Fabio Quartararo.
"Alex has been away from the MotoGP paddock for a while due to the injury he sustained at Mugello, but we are confident that he should be fully recovered and up to speed for the 2024 season," said team boss Lin Jarvis.
Morbidelli, 28, was championship runner-up to Spaniard Joan Mir in 2020 when he won three grands prix but he has not won a race since then. He starts this weekend's British Grand Prix 11th in the standings, two places behind Quartararo.
"It's a shame that the last two years didn't play out the way we both wanted and hoped for," said Jarvis.
"We discussed the possibilities to continue our partnership, but ultimately we decided that 2024 would be a moment to make a change, both for Yamaha and for Franky."
