I had this same error, and once I manually added the following dependency to the automation tool csproj file (Engine\Source\Programs\AutomationTool\AutomationTool.csproj), and rebuilt it the error disappeared:
<Reference Include="AWSSDK.S3">
<HintPath>..\..\..\Binaries\ThirdParty\AWSSDK\AWSSDK.S3.dll</HintPath>
<Private>true</Private>
</Reference>