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This is answered on this other Re:Post question. The short answer is that, no, CloudFront will not (at this time) use IPv6 to connect to an IPv6-only origin. So you can allow direct connections to the EC2 instance, and regulate that through Security Groups, NACLs, and host-based firewall rules (e.g., ipfilter or ipfw). The other answer points to the definitive page where you can look up IPv6 support by service. So while this is true at the time of writing, you can expect IPv6 support to improve over time, and those pages are the way to figure out whether IPv6 is possible.
Amazon CloudFront now supports IPv6 origins for end-to-end IPv6 delivery
https://aws.amazon.com/blogs/networking-and-content-delivery/amazon-cloudfront-now-supports-ipv6-origins-for-end-to-end-ipv6-delivery/
This is supported now. https://docs.aws.amazon.com/AmazonCloudFront/latest/DeveloperGuide/cloudfront-enable-ipv6.html
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Everything is working fine after pointing subdomain to IPV6 (AAAA recod), but using ipv6 only subdomain as origin, CloudFront is not responding ipv6 only instance