At the moment ApplePay does not support CloudFlare SSL/TLS.
In order to turn off the Cloudflare SSL, please, follow these steps:
- Log in to the Cloudflare dashboard and select your account.
- Select your domain.
- Go to SSL/TLS > Edge Certificates.
- For Disable Universal SSL, select Disable Universal SSL.
- Read the warnings in the Acknowledgement.
- Select "I Understand" and click Confirm.
Also kindly find list of Ciphers to properly set up your ApplePay and choose the corresponding SSL certificate here.