*UPDATED with new screenshots of Office 365 generator

You can use this free tool to create a Office 365/2016 MSI in order to deploy it with Microsoft Intune.

https://officedev.github.io/Office-IT-Pro-Deployment-Scripts/XmlEditor.html

Office 365 install generator
Click Install Generator
launch
Launch it and install it
Start New
Click Start New
2
Select 32 bit if a fresh install, if you have 32 bit installed you can not select 64 bit.
3
Feel free to add a lanugage
5
Just click Next
6
Remove stuff you do not want
7
Ensure you have the right edition or mabye you want to add 64 bit?
8
Of course you want automatic updates. Click next
9
Make it real silent. Don’t do Auto Activate
10
NEW: Self signing certificate. Remember to check and generate. If you do not do this there will be a UAC prompt
11
Could be anything
12
Give it a name and click save

 

You can manually sign the MSI

Or simply Deploy it to Microsoft Intune using the MDM channel.