Multisite is setup to do this by default. If you simply install the plugin without ‘network activating’ it, you are able to limit the use to any single site in the network.
To do this, you must be logged in with an account with super-admin rights. Install the plugin on the single-site dashboard > plugins; not from the network admin plugins page.
https://codex.wordpress.org/Multisite_Network_Administration#Plugins
Refer to the Site Specific section for complete details.