The Padres added right-handed pitchers Nick Vincent, left-handed pitchers Juan Oramas, Jose De Paula, Pedro Hernandez, infielder Edinson Rincon and outfielder Rymer Liriano.
The Padres' 40-man roster is now full.
"I think with five guys from our Latin America program [added] that it's a great milestone for Randy Smith and his staff," Byrnes said. "They have a lot to be proud of."
Liriano, an outfielder who is regarded by Byrnes as the Padres' top prospect, was the Most Valuable Player of the Midwest League last season. He hit .319 in 116 games with 12 home runs, 62 RBIs and 65 stolen bases.
Rincon, a third baseman, hit .328 with eight home runs and 51 RBIs, mostly playing for Class A Lake Elsinore.
On the pitching side, Oramas was 10-6 with a 3.49 ERA and 106 strikeouts over 108 1/3 innings between Triple-A Tucson and Double-A San Antonio.
Vincent is coming off a big season with San Antonio, going 8-2 with a 2.27 ERA in 66 appearances. He allowed 54 hits in 79 1/3 innings logging critical innings for MiLB's Minor League team of the year.
Hernandez was a combined 10-3 with a 3.49 ERA for three Minor League teams while De Paula (10-5, 5.22 ERA at Lake Elsinore) was also protected.
Not protected on Friday were two notable players -- 2007 first-round Draft pick, left-handed pitcher Nick Schmidt, and first baseman Matt Clark..
Schmidt, the 23rd-overall pick of the 2007 First-Year Player Draft, had a 3.91 ERA for two teams in 2011, and had a 5.40 ERA in his first eight appearances in the Arizona Fall League.
Clark hit .292 with 23 home runs and 83 RBIs with Tucson.
The Padres have a logjam at first base with prospect Anthony Rizzo, Kyle Blanks and Jesus Guzman all seeing time there in 2010. Veteran Mark Kotsay, who agreed to a one-year deal with the team on Wednesday, is an outfielder by trade but can also play some first base.
Also Friday, right-handed pitcher Jeremy Hefner was claimed off waivers by the Pirates.
Hefner struggled in his first full season at the Triple-A level, going 9-7 with a 4.98 ERA in the hitter-friendly Pacific Coast League. Opposing batters hit .283 against him.
Another pitcher, right-hander Andrew Carpenter, was claimed by the Jays. Carpenter was acquired off waivers from the Phillies on Sept. 2. He pitched in six games and had an 8.44 ERA.
The Rule 5 Draft is set for Dec. 8 on the final day of the Winter Meetings in Dallas.