Rafferty's inclusion was one of three changes made to the starting XI by PNE manager Ryan Lowe for the visit to the Liberty Stadium.
Ched Evans and Greg Cunningham came into the team, with Scott Sinclair moving to the bench, Andrew Hughes suspended and Brad Potts injured.
In last Tuesday night's 2-2 draw with Sheffield United, Rafferty had come on as a half-time substitute in place of Potts.
His previous action this season had come in the Carabao Cup, with him only added to the 25-man squad in October.
On the bench there was a return after a knee injury for midfielder Ryan Ledson, while Matthew Olosunde got a substitute's slot too.
It was Olosunde's first involvement in a matchday squad since December 4 - his one appearance to date in a PNE shirt came that day at Blackburn.
Swansea: Hamer, Cabango, Naughton, Manning, Christie, Downes, Grimes, Latibeaudiere, Smith, Ntcham, Piroe. Subs: Fisher, Bennett, Fulton, Obafemi, Wolf, Joseph, Walsh.
PNE: Iversen, Van Den Berg, Bauer, Cunningham, Whiteman, Rafferty, Browne, Johnson, Barkhuizen, Riis, Evans. Subs: Ripley. Lindsay, McCann, Ledson, Olosunde, Maguire, Sinclair..
Referee: Josh Smith (Stamford)
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