Coach Joachim Loew informed the players Wednesday at their training camp on the Spanish island of Mallorca shortly ahead of the midday deadline for all the 16 finalist teams to lodge their squads with UEFA.
"It was a difficult decision for the training staff," Loew said in a statement released by the German Football Federation.
All three players deserved to be in the squad during the June 7-29 tournament in Austria and Switzerland, he said. They had all done well in training and had "good prospects" after the tournament.
Helmes, a striker for Cologne, Schalke midfielder Jones and Marin, a midfielder with Borussia Moenchengladbach, all played a part in Germany's 2-2 draw with Belarus in Kaiserslautern on Tuesday.
It was a first cap for 19-year-old Marin, who most observers believed would clinch a place in the squad.