Starace, ranked 293 after reaching 27th on the ATP computer in 2007, needed nearly two-and-a-quarter hours to get past Stepanek, whom Federer beat last week in the second round in Madrid.
Starace had lost both of his previous matches with the 34-year-old Czech, who underwent surgery in January to relieve pressure on a nerve in his neck
Federer holds a 6-0 record over Starace, beating the home player in Rome at the Foro Italico in 2006 and earning a straight-sets victory in their last meeting indoors in Basel in 2011.
While leading seeds waited to get started in the second round after byes, the big names at the joint event filled up the practice courts at the last-chance tune-up week prior to the start of the French Open on May 26.
France's Benoit Paire earned a second-round spot at the expense of Argentine Juan Monaco 7-6 (7/4), 1-6, 6-4 while Spaniard Albert Ramos defeated Czech Jan Hajaek 7-5, 6-0. Russian Alex Kuznetsov advanced as Belgian veteran Xavier Malisse quit their match trailing 6-2, 3-1.
In women's play, Germany's Sabine Lisicki beat American Madison Burdette 6-1, 6-2, but German sixth seed Angelique Kerber withdrew prior to her opening match with an abdominal injury and was replaced by Lourdes Dominguez Lino of Spain.
China's Peng Shuai defeated Romanian Monica Niculescu 4-6, 6-3, 6-2 while Italian Nastassja Burnett put out 2008 finalist Alize Cornet of France 6-2, 6-2.
Results from the first day of the ATP Rome Masters and WTA Madrid Open on Monday (x denotes seeding):
Men:Albert Montanes (ESP) bt Martin Klizan (SVK) 3-6, 7-5, 6-3
Fabio Fognini (ITA) bt Andreas Seppi (ITA) 6-4, 6-1
Benoit Paire (FRA) bt Juan Monaco (ARG) 7-6 (7/4), 1-6, 6-4
Jerzy Janowicz (POL) bt Santiago Giraldo (COL) 7-5, 6-2
Albert Ramos (ESP) bt Jan Hajaek (CZE) 7-5, 6-0
Potito Starace (ITA) bt Radek Stepanek (CZE) 4-6, 6-4, 6-3
Andrey Kuznetsov (RUS) bt Xavier Malisse (BEL) 6-2, 3-1, retired
Marin Cilic (CRO X11) BT Andrey Golubev (KAZ) 6-4, 6-2
Ernests Gulbis (LAT) bt Jarkko Nieminen (FIN) 6-2, 7-6 (8/6)
Women:
Jelena Jankovic (SRB) bt Tsvetana Pironkova (BUL) 6-3, 6-0
Sabine Lisicki (GER) bt Madison Burdette (USA) 6-1, 6-2
Peng Shuai (CHN) bt Monica Niculescu (ROM) 4-6, 6-3, 6-2
Ayumi Morita (JPN) bt Sorana Cirstea (ROM) 6-1, 6-3
Samantha Stosur (AUS x9) bt Hsieh Su-Wei (TPE) 6-2, 6-3
Nastassja Burnett (ITA) bt Alize Cornet (FRA) 6-2, 6-2
Garbine Muguruza (ESP) bt Mathilde Johansson (FRA) 1-6, 6-0, 6-2
Melanie Oudin (USA) bt Ekaterina Makarova (RUS) 2-6, 7-5, 4-2, retired
Laura Robson (GBR) bt Venus Williams (USA) 6-3, 6-2