The 29-year-old has spent six years with the La Liga outfit and played the full 90 minutes as they kicked off the new campaign with a 3-1 defeat at Celta Vigo.
However, Rafa has now been deemed surplus to requirements at Coliseum Alfonso Perez, with Bundesliga new boys Paderborn opting to add him to their defensive ranks.
"We've had our eyes and ears open for some time to strengthen the defence," said general manager Michael Born. "I'm very pleased that the intensive negotiations with Getafe have led to a good result."
Coach Andre Breitenreiter is equally happy with the new addition as Paderborn look to retain their top-flight status.
"Rafa is a player who can help us immediately with his experience and his footballing education; he can give our team more stability, [which] we desperately need in the Bundesliga," added Breitenreiter.
Paderborn are unbeaten in the league so far this season, having drawn 2-2 with Mainz before winning 3-0 at Hamburg.
