GitHub: How can I close the two issues with commit message?

git commit -m "Closes #1, closes #2, closes #3; rest of commit message."

You can use any of these keywords to close an issue via commit message:

close, closes, closed, fix, fixes, fixed, resolve, resolves, resolved

The message MUST contain a string matching the following pattern: KEYWORD #ISSUE. For example: close #1.

How can I close two or more issues with commit message?

You can use comma separated list in the commit message for it.

See this link for more information.

It is also possible to close several issues in the same commit: just repeat several time the pattern to close issues. For example, the following commit message: add new quick sort algorithm, fixes #4, resolve #6, closed #12 would close, the issues 4, 6 & 12 of the project on which the commit would occur.

You can try:

git commit -m "closes #1, closes #2, closes #3; YOUR COMMIT MESSAGE"

EDIT:

Adding a link from docs.github.com.

You can link a pull request to an issue by using a supported keyword in the pull request's description or in a commit message (please note that the pull request must be on the default branch).

close, closes, closed, fix, fixes, fixed, resolve, resolves resolved