Nef has not played for his country since their stunning 2-1 home loss to Luxemburg just under a year ago, the last time the Swiss have lost a game. He plays for Triestina in the Italian second division.
Eintracht Frankfurt midfielder Pirmin Schwegler, given a first callup under the leadership of Ottmar Hitzfeld for last month's goalless draw with Italy, kept his place in the squad.
Switzerland, unbeaten in their last seven games, face Greece in a top-of-the-table clash in European Group Two in Basel. Both teams have 13 points from six outings.
The same squad will travel to Riga for another qualifier against Latvia four days later.
Defender Philipp Degen, who is struggling for a game at Liverpool, was left out along with Arsenal's Johan Djourou.
Squad:
Goalkeepers: Diego Bengalio (VfL Wolfsburg), Johnny Leoni (FC Zurich), Marco Woelfli (Young Boys Berne)
Defenders: Stephane Grichting (Auxerre), Stephan Lichtsteiner (Lazio), Ludovic Magnin (VfB Stuttgart), Alain Nef (US Triestina), Philippe Senderos (Arsenal), Christoph Spycher (Eintracht Frankfurt), Steve Von Bergen (Hertha Berlin)
Midfielders: Tranquillo Barnetta (Bayer Leverkusen), Eren Derdiyok (Bayer Leverkusen), Gelson Fernandes (St Etienne), Benjamin Huggel (Basel), Marco Padalino (Sampdoria), Pirmin Schwegler (Eintracht Frankfurt), Marco Streller (Basel), Goklan Inler (Udinese)
Forwards: Alexander Frei (Basel), Johan Vonlanthen (FC Zurich), Blaise Nkufo (Twente Enschede), Hakan Yakin (Luzern)
