It also earned Southampton manager Harry Redknapp his first win since moving to St Mary's, but he will be looking for more of the same in the league.
Phillips should have put Saints in front within a minute, volleying over from six yards from David Prutton's cross and Calum Davenport should have done better with a far-post header after Phillips put the ball into the box in the 25th minute.
In between Southampton keeper Antti Niemi had to be alert to dash out to the edge of the box to foil Scott McGleish after he pounced on some indecision in the Saints defence.
But Phillips shot Southampton into a 29th minute lead, turning to volley home first time after Peter Crouch headed the ball on into the strikers path. However, Saints lead lasted just 60 seconds as Lee Williamson found space 25 yards out to beat Niemi with a fierce shot into the far corner.
Northampton then enjoyed their best spell of the match with winger Josh Low causing problems with his pace on the right flank. Twice in quick succession Low forced his way into the area only to be denied by Niemi on each occasion.
But a quick counter-attack saw Crouch restore Southampton's advantage four minutes before the break, running on to Phillips' through ball to beat Lee Harper.
Niemi was almost caught out by a McGleish header on the stoke of half-time as Northampton looked to draw level for the second time.
But a third goal eight minutes after the restart settled the tie with Phillips once again involved.
Another quick break ended with Phillips reaching the by-line and pulling the ball back with Jamie Redknapp to score his first goal for the club.
Harper then kept the Cobblers in the tie when he denied Phillips from a direct free-kick but Niemi was again called into action in the closing stages, making a double save from substitute Eric Sabin and Martin Smith, while also denying Trevor Benjamin in the final minute.
Man of the Match: Kevin Phillips – The former England striker was at his best to score one goal and set up the other two as the Premiership side proved too hot for the Cobblers.