Sublime does not use the shebang to determine the execution, it uses your build rule. You could customize the Python build rule to add variants for python2 and python3.
- Official instructions for adding build variants.
- Simplified example of build variants from another SO question.
Note that with build variants, the default is run by Command+B (Mac) or Control+B (Windows and Linux). The second variant can be run Command+Shift+B (Mac) or Control+Shift+B (Windows and Linux).