Hoeger was excluded from the squad over loyalty concerns last week after Schalke also released Kevin-Prince Boateng and Sidney Sam following a poor run of form after the winter break that had put their European hopes in jeopardy.
"Marco Hoeger can be part of the Royal Blues' squad for the last match day on Saturday," the club said in a statement on Tuesday.
"Following discussions between the midfielder and the sporting director on Monday, he can now return to training and matches."
Last week's 1-0 victory over Paderborn ensured fifth-placed Schalke's qualification for next season's Europa League.
The narrow win secured a top-six finish while Hamburg face the prospect of a first-ever relegation even if they beat the Ruhr valley club, as they need results involving teams around them to go their way.
(Reporting by Karolos Grohmann; Editing by John O'Brien)
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