Well, I found a workaround:

  1. Add new Git installation in global settings.
  2. In the job configuration, got to "Source Code Management -> Git -> Advanced..." and select the above installation as Git executable.
  3. Trigger new build.

The new build should now be able to clone using git.

Somehow, creating a new Git installation (global config) and choosing that installation as Git executable (job config) propagated the proper settings to the job.

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