Police were urgently in pursuit of Ali Bashar, a 20-year-old Iraqi who flew to Erbil in northern Iraq days after the girl's disappearance.
Bashar is believed to have arrived in Germany in 2015 via Turkey and Greece, along with a wave of other refugees. He was a suspect in a string of previous offenses in the area, including a robbery at knifepoint.
An Iraqi migrant suspected of the rape and murder of a 14-year-old girl in western Germany was arrested by Kurdish forces in Iraq one day after German police issued an global warrant for his arrest.
A 13-year-old refugee boy told Police in Wiesbaden on Sunday about a girl who had been raped and murdered, and named Bashar as the perpetrator.
Wiesbaden senior public prosecutor Oliver Kuhn told reporters that both suspects "lived in refugee centers in Wiesbaden", a city on the Rhine river across from Mainz. It called for a thorough investigation and warned in a statement against "premature conclusions".
Some German Jews have expressed concern about a perceived rise in anti-Jewish prejudice with the influx of mainly Muslim migrants, although German police blame most anti-Semitic incidents on followers of the German far-right. Police said they believe she had been strangled to death.
Seehofer announced the news of the suspect's subsequent arrest during a hastily-convened press conference in the town of Quedlinburg.
Politicians from across the political spectrum called for a comprehensive investigation, including into how it was possible for the Iraqi man to flee Germany with his parents and siblings under what police said were false names.
It is not clear what motives the suspects pursued and whether the rape and murder will be investigated as a hate crime.
In Bild, a tabloid that printed a grisly alleged timeline of the crime, the Social Democrats' interior expert, Burkhard Lischka, said the questionable travel documents coupled with the destination should have been a red flag for immigration officers at Düsseldorf airport.
'The only thing that is worse than the murder of a child is the murder of a child by a criminal who should not have been in our country.
The Turkish suspect, who wasn't previously known to police, was arrested on Wednesday evening. Frankfurter Allgemeine Zeitung said "these cases seem to be adding up" and Tagesspiegel said that it was "particularly sad" that the victims were "interested, curious and. tried to befriend" migrants.