Both will see out this weekend's Belgian Grand Prix before departing the Enstone squad, while Pat Fry has left to join Williams.
Szafnauer joined Alpine 18 months ago, replacing Marcin Budkowski, while Permane has been with the organisation for 34 years.
It comes shortly after Laurent Rossi's reappointment within the broader Renault organisation to “focus on special projects linked to the group's transformation.”
Philippe Krief has been appointed the Alpine brand's new CEO.
“With Otmar and with Alan, it's the same,” said Famin.
“We thank them for all they brought to the team, for a very long time for 34 years in Enstone, and more recently with Otmar.
“But we were not on the same line on the timeline to recover the level, of which the level of performance we were aiming for.”
The Enstone operation has been in a period of transition, arguably since the end of 2020 when Daniel Ricciardo and former team boss Cyril Abiteboul departed the team – Alain Prost departed around the same time.
That saw Rossi come into the fold as the team was rebranded Alpine for 2021, with a complicated three-pronged management structure that included Budkowski and Davide Brivio.
Budkowski left the organisation in 2022, with Szafnauer joining soon after.
Midway through last season it was embroiled in a contract scuffle over the services of Oscar Piastri, with the contract recognition board revealing there was no contract in place with the Australian – an embarrassing moment for the organisation.
This year, though there have been moments of promise, it has remained inconsistent and heads into this weekend off the back of two double-DNFs.