You should check the certificate shown to clients when accessing your domain. I think you'll find that it is not the certificate that you created outside of Cloudflare. Cloudflare doesn't need your private key as they issue a certificate for your domain to themselves and use that for the connection with the client. The certificate you created is used between Cloudflare and your server. The only option I'm aware to route traffic through Cloudflare where they don't terminate SSL is an enterprise only feature.
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