The Padres had the third pick and selected shortstop Allen Cordoba from the St. Louis Cardinals.
But they also lined up trades with Minnesota and Cincinnati to acquire the top two Rule 5 selections -- right-handed pitcher Miguel Diaz and catcher Luis Torrens, respectively -- which became official after the Draft.
Minnesota drafted Diaz from the Minor League system of the Brewers with the first selection. The Reds drafted Torrens from the Yankees organization with the second pick.
Diaz was then shipped to the Padres for right-handed pitcher Justin Haley, who San Diego acquired earlier Thursday from the Angels, and a player to be named later or cash considerations.
Torrens was acquired for a player to be named later and cash considerations.
The Padres did not lose any players in the Major League portion of the Rule 5 Draft. They now must keep Cordoba, Diaz and Torrens on their Major League roster for the duration of the 2017 season, or else they will be returned to their original teams.
Right-handed starter Luis Perdomo came to the Padres in the 2015 Rule 5 Draft. Three other players acquired by the Padres during that Draft were returned to their original teams.
Diaz, 22, is a native of the Dominican Republic. The 6-foot-1, 175-pounder was 1-8 with a 3.71 ERA in 26 games (15 starts) with Class A Wisconsin in 2016. Diaz allowed 83 hits and 29 walks with 91 strikeouts in 94 2/3 innings last season, recording a 1.183 WHIP and a 3.1-to-1 strikeout-to-walk ratio.
Torrens, 20, is a 6-foot, 175-pound, right-handed hitter from Venezuela. He split the 2016 season between Class A Charleston and short-season Class A Staten Island, hitting .250/.350/.337. He collected 15 RBIs, 10 doubles and two homers.
Cordoba, 21, is a 6-foot-1, 175-pound right-handed hitter from Panama. He led the Appalachian Rookie League with a .362 batting average last season. He also led the league in hits (71), was third with 22 steals and fourth with a .427 on-base percentage. In addition to 21 walks, Cordoba had 16 doubles and five triples, with a .922 OPS.
Cordoba was a postseason All-Star of both the Appalachian League in 2016 and the Gulf Coast Rookie League in 2015, when he hit .342 with a .401 on-base percentage in 53 games.
Given their positions, all three have a feasible shot of making the Padres' Major League roster.
With Christian Bethancourt getting a chance to be a catcher-pitcher-outfielder hybrid, the Padres might keep a third catcher as an additional backup to Austin Hedges. Although Luis Sardiñas and Jose Rondon are currently the leading candidates at shortstop, the position is open, and the Padres are still looking for help.
And Perdomo last year showed what a Rule 5 pitcher can do. He went 9-10 with a 5.71 ERA in 35 games (20 starts), but posted a 4.30 ERA in the second half.
Additionally, the Padres selected right-handed pitcher Trevor Frank from the Cleveland Indians in the Triple-A round of the Rule 5 Draft Thursday. The El Cajon, Calif. native was Cleveland's eighth-round pick in 2013 out of UC Riverside.
Frank, who missed most of the 2015 season with an elbow strain, returned in 2016 with a 2.47 ERA in 44 relief appearances at High Class A Lynchburg last season, along with 17 saves. He had an 0.92 WHIP and .191 opponents' batting average, with 43 strikeouts against 10 walks in 43 2/3 innings.