Hello @alex_viale
Workflows determine how your issues can move from one status to another. The Automations that are added there execute within the context of a status change for an issue.
The Automations feature enables you to create automation rules triggered by a variety of events; status change, change of values of fields, comment added/deleted/updated, worklog added/deleted/updated, and so on. The rule can also be created so that they run on a scheduled basis, or can be triggered manually by a user.
That's the primary difference.
Also, Automation Rules are, I believe capable of a great deal more than the automations you can natively add within a Workflow.
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