It will not be the first time Merkel has sat in the stands for a Germany game. She attended the 2010 World Cup and a Euro 2012 qualifier against Turkey, where she was photographed with bare-topped midfielder Mesut Ozil in the changing room after the match.
"The team is delighted with the news and she is our lucky charm," said team spokesman Harald Stenger on Wednesday.
German and Greek players and coaches have sought to play down the importance of a game which has turned minds at the tournament to a deepening economic crisis affecting many of the nations involved.
But Greek media have relished the prospect of sending a fancied German team home in front of the chancellor, who is a deeply unpopular figure for the tough austerity she has imposed on the country in exchange for its international bailout.
In line with other European leaders, Merkel did not attend any of Germany's group games due to a diplomatic boycott of Ukraine in protest at the jailing of former prime minister Yulia Tymoshenko.
Berlin spokesman Georg Streiter said the chancellor had accepted an invitation from Polish Prime Minister Donald Tusk to attend the game in the Baltic coast city.
Pressed on whether Merkel would meet Antonis Samaras, who is working to form a new Greek government after his New Democracy party won elections at the weekend, Streiter joked: "Maybe in the halftime break."
German Finance Minister Wolfgang Schaeuble, also a detested figure in Greece, told Die Zeit newspaper he thought Germany would win 3-1.
"The Greeks played fantastically against Russia (in their last game). It won't be an easy game. However, the German squad is in peak form," he said.