The team also designated right-handed pitcher Cory Burns for assignment. The moves give the Padres a full 40-man roster.
Major League Baseball's deadline to protect players was Tuesday at 8:59 p.m. PT. Players who were first signed at the age of 18 must be added to 40-man rosters within five years or they become eligible to be drafted by other organizations in the Rule 5 Draft. Those players who were signed at age 19 need to be protected within four years.
The Rule 5 Draft is set for Dec. 6 during the Winter Meetings in Nashville, Tenn.
Portillo, a 20-year-old right-hander who is ranked No. 7 among the Padres' top prospects, was 8-11 with a 3.34 ERA over 26 starts in 2012 between Class A Fort Wayne and Double-A San Antonio. He was 6-6 with a 1.87 ERA in 18 starts for Fort Wayne before earning a promotion -- skipping Class A Advanced Lake Elsinore -- for San Antonio.
Asencio, 23, hit .323 with eight home runs and 61 RBIs in 92 games for Fort Wayne. He won the Midwest League batting title. Asencio is a .306 hitter in parts of three seasons in the Padres' organization.
Decker, 22, hit .201 in 56 games in 2012 with rookie-level Peoria and San Antonio. A foot injury cost him much of his season. Decker, the 42nd overall pick in 2008, is a career .264 hitter in parts of his five years in the Padres' system.
Burns, 25, made his Major League debut with the Padres in 2012, going 0-1 with a 5.50 ERA over 17 appearances. He spent most of the season with Triple-A Tucson, going 1-2 with a 3.14 ERA in 54 games.
Also, the Padres on Monday agreed to a pre-arbitration deal with outfielder Kyle Blanks that will be worth $605,000. Blanks played in four games with the Padres last season before landing on the disabled list April 14 with a strained left shoulder. On May 2, he had season-ending arthroscopic surgery.