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The connection between your git repository and a remote repository is done via the "git remote" settings of your repository.
SourceTree just uses this repository settings to connect to the remote repository. So configuring a remote repository on your own server as a git remote for your local repository, you can use SourceTree to perform push, pull and fetch operations.
Some more sophisticated functionality in SourceTree might not be available (for example listing all repositories on your own server within SourceTree - as for example your Server might not provide this information)