Cloudformation template for a VPC with ipv6, with public and private subnets, calculating the subnet ipv6 CIDR blocks on the fly.

vpc.yaml

---
AWSTemplateFormatVersion: '2010-09-09'
Description: Public VPC and subnets

Resources:

  #
  # Public VPC
  #
  PublicVpc:
    Type: AWS::EC2::VPC
    Properties:
      CidrBlock: 172.31.0.0/16
      InstanceTenancy: default
      Tags:
      - Key: Name
        Value: Public VPC
  IPv6CidrBlock:
    Type: AWS::EC2::VPCCidrBlock
    Properties:
      VpcId: !Ref PublicVpc
      AmazonProvidedIpv6CidrBlock: true

  #
  # Internet gateways (ipv4, and egress for ipv6)
  #
  InternetGateway:
    Type: AWS::EC2::InternetGateway
    Properties:
      Tags:
      - Key: Name
        Value: Public VPC Internet Access
  InternetGatewayAttachment:
    Type: AWS::EC2::VPCGatewayAttachment
    Properties:
      VpcId: !Ref PublicVpc
      InternetGatewayId: !Ref InternetGateway
  EgressOnlyInternetGateway:
    Type: AWS::EC2::EgressOnlyInternetGateway
    Properties: 
      VpcId: !Ref PublicVpc

  #
  # Routing - public subnets
  #
  PublicSubnetRouteTable:
    Type: AWS::EC2::RouteTable
    Properties:
      VpcId: !Ref PublicVpc
      Tags:
      - Key: Name
        Value: Route Table for Public Subnets in Public VPC
  PublicSubnetDefaultRoute:
    DependsOn: InternetGatewayAttachment
    Type: AWS::EC2::Route
    Properties:
      DestinationCidrBlock: 0.0.0.0/0
      RouteTableId: !Ref PublicSubnetRouteTable
      GatewayId: !Ref InternetGateway
  PublicSubnetDefaultIpv6Route:
    Type: AWS::EC2::Route
    Properties:
      DestinationIpv6CidrBlock: ::/0
      RouteTableId: !Ref PublicSubnetRouteTable
      EgressOnlyInternetGatewayId: !Ref EgressOnlyInternetGateway

  #
  # Routing - private subnets
  #
  PrivateSubnetRouteTable:
    Type: AWS::EC2::RouteTable
    Properties:
      VpcId: !Ref PublicVpc
      Tags:
      - Key: Name
        Value: Route Table for Private Subnets in Public VPC
  PrivateSubnetDefaultIpv6Route:
    Type: AWS::EC2::Route
    Properties:
      DestinationIpv6CidrBlock: ::/0
      RouteTableId: !Ref PrivateSubnetRouteTable
      EgressOnlyInternetGatewayId: !Ref EgressOnlyInternetGateway

  #
  # Access control   
  #
  PrivateSubnetsNetworkAcl:
    Type: AWS::EC2::NetworkAcl
    Properties:
      VpcId: !Ref PublicVpc
      Tags:
      - Key: Name
        Value: Private Subnet on Public VPC ACL
  PrivateSubnetsNetworkAclInboundEntry:
    Type: AWS::EC2::NetworkAclEntry
    Properties:
      NetworkAclId: !Ref PrivateSubnetsNetworkAcl
      RuleNumber: 1
      PortRange: 
        From: 22 # SSH
        To: 22
      Protocol: 6 # TCP
      RuleAction: allow
      Egress: false
      CidrBlock: 172.31.0.0/16
  PrivateSubnetsNetworkAclIpv6OutboundEntry:
    Type: AWS::EC2::NetworkAclEntry
    Properties:
      NetworkAclId: !Ref PrivateSubnetsNetworkAcl
      RuleNumber: 1
      Protocol: -1
      RuleAction: allow
      Egress: true
      Ipv6CidrBlock: ::/0
  PrivateSubnetsNetworkAclOutboundEntry:
    Type: AWS::EC2::NetworkAclEntry
    Properties:
      NetworkAclId: !Ref PrivateSubnetsNetworkAcl
      RuleNumber: 2
      Protocol: -1
      RuleAction: allow
      Egress: true
      CidrBlock: 0.0.0.0/0

  #
  # Public subnet A   
  #
  PublicSubnetA:
    Type: AWS::EC2::Subnet
    Properties:
      CidrBlock: 172.31.0.0/20
      Ipv6CidrBlock: 
        Fn::Sub:
          - "${VpcPart}${SubnetPart}"
          - SubnetPart: '01::/64'
            VpcPart: !Select [ 0, !Split [ '00::/56', !Select [ 0, !GetAtt PublicVpc.Ipv6CidrBlocks ]]]
      AvailabilityZone: !Select [ 0, !GetAZs '' ]
      VpcId: !Ref PublicVpc
      MapPublicIpOnLaunch: 'true'
      Tags:
      - Key: Name
        Value: Public Subnet A
  PublicSubnetARouteTableAssociation:
    Type: AWS::EC2::SubnetRouteTableAssociation
    Properties:
      RouteTableId: !Ref PublicSubnetRouteTable
      SubnetId: !Ref PublicSubnetA

  #
  # Private subnet A   
  #
  PrivateSubnetA:
    Type: AWS::EC2::Subnet
    Properties:
      CidrBlock: 172.31.48.0/20
      Ipv6CidrBlock: 
        Fn::Sub:
          - "${VpcPart}${SubnetPart}"
          - SubnetPart: 'a1::/64'
            VpcPart: !Select [ 0, !Split [ '00::/56', !Select [ 0, !GetAtt PublicVpc.Ipv6CidrBlocks ]]]
      AssignIpv6AddressOnCreation: true
      AvailabilityZone: !Select [ 0, !GetAZs '' ]
      VpcId: !Ref PublicVpc
      Tags:
      - Key: Name
        Value: Private Subnet A in Public VPC
  PrivateSubnetAAclAssociation:
    Type: AWS::EC2::SubnetNetworkAclAssociation
    Properties:
      NetworkAclId: !Ref PrivateSubnetsNetworkAcl
      SubnetId: !Ref PrivateSubnetA
  PrivateSubnetARouteTableAssociation:
    Type: AWS::EC2::SubnetRouteTableAssociation
    Properties:
      RouteTableId: !Ref PrivateSubnetRouteTable
      SubnetId: !Ref PrivateSubnetA

Thanks for the suggestions! Indeed, using the newer Fn::Cidr function and adding DependsOn would be a nice addition. I'm glad this helped some of you out!