Eye strain is not an serious eye diseases. It is just a symptom of tiredness especially for people have their eyes get tired from intense use such as reading, or working at the computer for extended period. So, eye strain shall not be the causes of headaches. But from your description, you got headaches because of tiredness. So, stop your work and take a rest can help your relieve from eye strain and headaches.
Eye strains is a common symptom that often happen to people who need work at computer for an extended period. In common, eye strain is harmless. Taking eye breaks can help you relieve eye strain. And people with eye strain possible to feel difficult to concentrate, and to cause headaches. As long as you take a rest, eye strain and headaches will gone. So, don't worry.