I was able to solve this.
Navigate to your Sitecore Azure Toolkit path in Powershell and run the following after unblocking all the files.
- Import-Module .\tools\Sitecore.Cloud.Cmdlets.psm1
- Import-Module .\tools\Sitecore.Cloud.Cmdlets.dll
And now we can use the commands to create the WDP for the Sitecore Module like Data Exchange Framework by running this command.
ConvertTo-SCModuleWebDeployPackage -Path "C:\Sc DEF Packages for Sc9U1\Data Exchange Framework 2.0.1 rev. 180108.zip" -Destination "C:\WDP"
After the script run you can inspect the scwdp.zip file generated and check if it already contains the dacpac and the other contents of the module.
Everything is now set and create your azuredeploy.json for this package and update your azuredeploy.parameters.json to add this in the modules node item.