- Go to the category page you want to change canonical URL in Magento Admin
- Click the tab “Custom Design”
- In the Custom Layout Update text box, paste this:

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<reference name="head">
    <action method="removeItem" block="head">
        <item>link_rel</item>
        <name>http://loca.lho.st/old-canonical-url</name>
    </action>
    <action method="addLinkRel" translate="title">
        <rel>canonical</rel>
        <href>http://loca.lho.st/new-canonical-url</href>
    </action>
</reference>

Change http://loca.lho.st/old-canonical-url and http://loca.lho.st/new-canonical-url with your desired URLs and save the category.

Basically first action tag in the code removes old canonical URL and second action tag adds the canonical URL with the new value you specify.