Apple has rejected my application because Heroku does not support IPv6
Apple is not requiring that an application only communicate via IPv6, what they require, is that applications support IPv6-only networks in case the application is running within one.
For example, applications may not use an IPv4 address (ex. 0.0.0.0) in order to check for a network connection, as this will always fail in an IPv6 environment. A device running on an IPv6 network will have access to a NAT64 gateway which provides seamless access to IPv4 networks and is invisible to the device.
We recommend that you check out how your app manages it's networking and network requests, and then clarify the particular points with Apple if necessary. Note that using domain name-based resolution is almost always preferred over a static IP address, the latter of which being the most common failure we've seen with App Store submissions.