San Diego selected Eflin in the first compensation round of the Draft, using a pick they received when Heath Bell signed with Miami.
Eflin, the 33rd overall pick, pitched for Hagerty High School in Oviedo, Fla. The 6-foot-6, 215-pounder went 7-0 with a 0.51 ERA and was a first-team All-Central Florida selection. He had been in San Diego over the weekend taking a physical.
Having already locked up their first-round pick, left-hander Max Fried, the Padres have now signed their top two picks and 32 of 44 selections made in the Draft.
Teams have until July 13 to sign their picks.