The 29-year-old returns home after seven years in the Bundesliga and half a year in Bundesliga 2, having joined the Royal Blues from Kashima Antlers back in 2010.
He made 104 Bundesliga appearances, but injuries restricted him to just two outings in Bundesliga 2 this season. "Unfortunately, Atsuto was unable to show us what potential he has and that is why we've accommodated his wish of returning home," said Union Berlin sporting director Helmut Schulte.
Watch: Uchida's emotional goodbye from Gelsenkirchen
Capped 74 times by Japan, Uchida was given a stirring send-off from Schalke earlier this season. He won the DFB Cup with Schalke in 2011 and was part of the team which silenced the Estadio Santiago Bernabeu with a 4-3 win over Real Madrid in the Champions League in 2015, even if the hosts progressed on aggregate.
He will now look to add to his three Japanese J1 League titles, won with the Antlers in 2007, 2008 and 2009, and the 2007 Japanese Cup triumph.