You could use javascript to disable the button  when it was clicked and enable it when the job was done .

Have you tried disabling the button  after the first click  ?

The most simple way is to disable button  after click. To do this, add JavaScript event "onclick" like below:

<form>
<input id="submitButton" type="submit" value="Button" onclick="disableButton()"/>
</form>

<script type="text/javascript">
function disableButton()
{ document.getElementById("submitButton").disabled = true; }
</script>

If you need framework specific solutions, please let us know which framework do you use.
For example Struts2 has tokens to avoid this situations.

if you are using J2EE stack,
since you can not use synchronized keyword in EJB components,
you have to do it in other ways, here is one of them:

then use a statefull session bean for doing this task.
put a boolean variable in your bean,
in statefull session bean check this boolean variable before starting the task and set its value
look at this example:

public Class MySFSB .... {
...
boolean isBusy = false;
...
public myMethod(...) {
if (isBusy) {
// throw exception or do some thing else like just returning from method
return;
}
isBusy = true;
// now do your job
....
....
isBusy = false;
}

You can also check the state of process  on the client side
Disable the key after clicking and Enable it at the end of process.

HTTP Requests are designed to work asynchronously. Implement synchronous (Ajax) requests to handle it.