The sixth-placed Robins are now four points clear of MK Dons with only two fixtures remaining after mid-table Crewe made it too easy for them.
Rooney put Swindon ahead in the fifth minute when he turned in Aden Flint's header and Alex never seriously challenged the home team's dominance.
Massimo Luongo, on loan from Tottenham, got the second in the 18th minute after Gary Roberts had created the chance with a centre.
The match was over as a contest after 25 minutes when Rooney converted a Luongo corner - although Byron Moore hit the bar just before half-time.
Harry Davis scored his first goal of the season from the penalty spot for Crewe in the 65th minute after Max Clayton had been brought down by goalkeeper Wes Foderingham, who earned a yellow card.
Yet, six minutes later, the hosts added further gloss when striker James Collins robbed Michael West and found the net via the inside of a post.