If you view the EPUB in the Calibre viewer and the text is justified, then the resulting AZW3 will be as well—provided that the option for text justification is set to "Original" or "Justify text" in the Look & Feel conversion options. See attached image.
If the EPUB text is left aligned, then set the option to "Justify text". You can also open the EPUB in the editor (Edit Book) and manually change/add the text-align property for the appropriate classes in the CSS—as Katsunami pointed out. The former method is obviously the simpler of the two.
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