The breakthrough came with the hosts' first effort on goal after 16 minutes, Phillips' low, first-time drive from a Roland Idowu cross evading David Mitchell too easily for the goalkeeper's liking.
Unmarked, Phillips added his second - and fourth in two games - seven minutes before the break, side-footing home another low cross from his fellow midfielder.
Ayr, who knew they would qualify as runners-up unless they lost by nine or more goals after winning their opening three games, lacked a cutting edge and could not muster an attempt on target in a lacklustre first half.
St Mirren should have extended their lead when Mikael Mandron fired wastefully over the crossbar.
However, visiting manager Scott Brown's second-half changes invigorated Ayr and winger Dom Thomas curled a drive just wide before his corner was headed home by midfielder Kevin Holt.
Two more Thomas corners found fellow substitute George Oakley and Holt, but both headers were comfortably held by debutant goalkeeper Shamal George.
Although Mark O'Hara missed a late chance to restore the lead when the midfielder fired wide when clean through on goal, two goals were enough for St Mirren.
The Buddies' reward is a home tie against top-flight rivals Heart of Midlothian, while Ayr are away to fellow Championship side Partick Thistle.