Soto, the NL Rookie of the Year with the Cubs in 2008, appeared in just 24 games with Texas and Oakland last season. He was limited by knee and foot injuries and was also arrested on a marijuana possession charge.
Penny, an All-Star with the Los Angeles Dodgers in 2006 and 2007, was 2-1 with a 6.58 ERA in four starts and eight appearances with Miami last season.
Chicago also agreed Thursday to minor league deals with right-handed pitchers Jairo Asencio, Scott Carroll, Jesse Crain, Logan Kensing, Arcenio Leon and J.D. Martin; left-handers Zach Phillips and Joe Savery; catcher George Kottaras; infielders Juan Diaz and Andy LaRoche; and outfielders Tony Campana and Michael Taylor.