You can't do this with WiX natively.
What you can do however, is define your version as a variable. e.g.:
<Product Id="*"
UpgradeCode="$(var.Property_UpgradeCode)"
Name="!(loc.ApplicationName)"
Language="!(loc.Property_ProductLanguage)"
Version="$(var.version)"
Manufacturer="!(loc.ManufacturerName)" >
Then you can pass in the version number on the command line. Here's an example using Nant
<candle
out="${dir.obj}\"
rebuild="true"
extensions="WixUIExtension;WixNetFxExtension">
<defines>
<define name="ProcessorArchitecture" value="${release.platform}" />
<define name="SourceDir" value="${dir.source}" />
<define name="version" value="${version}" />
<define name="releasetype" value="${release.type}" />
<define name="Language" value="${language}" />
</defines>
<sources>
<include name="*.wxs" />
</sources>
</candle>
Then you just handle the version number in the same way you do for your application :)