Löw named an extended squad on May 16 for a training camp in Mallorca, but had to drop three players before submitting his final 23-man squad for the tournament, co-hosted by Austria and Switzerland, which begins on June 7.
Jones (Schalke 04), Helmes (Bayer Leverkusen) and Marin (Borussia Mönchengladbach) will all now return to their clubs.
"The decision made by our coaching team was a very difficult one," said Löw. "It was a millimetre decision, because every one of the three players earned their place in the Euro 2008 squad. The decision was especially hard as all three did well in the training
camp and will have a role to play in the national team after the tournament."
Löw singled out talented teenager Marin who had been promoted to the senior team after shining for Germany's Under-21 side. "Marko Marin is a player of huge talent who has a huge future, he has improved in the last week alone, I am sure we will hear of him in the future," said Löw.
All three played in Tuesday night's 2-2 draw with minnows Belarus and were told of the decision in a team meeting on Wednesday morning.
The most surprising omission was Marin as Löw had heaped praise on the teenager all week, but the youngster took the rejection in his stride having made his debut against Belarus.
"It was great for me just to be named in the 26-man squad," said Marin. "Of course, I dreamed about being involved in the European Championships. It is unfortunate that I am not going, but I have won my first cap and I am still very young. I hope I will be invited again and I will keep my fingers crossed for the boys."
Germany face Serbia in their final warm-up game in Gelsenkirchen on Saturday and open their Euro 2008 campaign against Poland in Klagenfurt on June 8.
Goalkeepers: Jens Lehmann (Arsenal/ENG), Robert Enke (Hanover 96), Rene Adler (Bayer Leverkusen)
Defenders: Christoph Metzelder (Real Madrid/ESP), Per Mertesacker (Werder Bremen), Philipp Lahm (Bayern Munich), Arne Friedrich (Hertha Berlin), Marcell Jansen (Bayern Munich), Clemens Fritz (Werder Bremen), Heiko Westermann (Schalke 04)
Midfielders: Michael Ballack (Chelsea/ENG), Thomas Hitzlsperger (VfB Stuttgart), Simon Rolfes (Bayer Leverkusen), Torsten Frings (Werder Bremen), Bastian Schweinsteiger (Bayern Munich), Piotr Trochowski (Hamburg), Tim Borowski (Werder Bremen), David Odonkor (Real Betis/ESP)
Forwards: Miroslav Klose (Bayern Munich), Lukas Podolski (Bayern Munich), Mario Gomez (VfB Stuttgart), Kevin Kuranyi (Schalke 04), Oliver Neuville (Borussia Moenchengladbach)