"The coach has his own ideas, I've got mine and as they don't meet, it doesn't make sense [to carry on]," said the 33-year-old Bayern Munich captain.
Helmer announced he was ending his international career as Vogts was preparing to name his squad for two friendlies against Malta and Romania early next month.
They will be Germany's first games since their quarter-final defeat by Croatia in the World Cup last month. After witnessing a disastrous performance from his ageing team in France, Vogts vowed to rebuild and steer Germany back into the world's elite.
Jurgen Klinsmann, and the defenders Jurgen Kohler, Stefan Reuter and Olaf Thon have all ended their international careers, and Vogts has already said he will not pick the veteran libero Lothar Matthaus for the Malta match.
The 36-year-old Andreas Kopke, who is sharing goalkeeping duties at Marseilles with the newcomer Stephane Porato, will also be left out of the national team, as Vogts has named Oliver Kahn as his new No 1.
Andreas Moller, the Borussia Dortmund midfielder, and Thomas Hassler both said on Saturday that Vogts had informed them they would not be picked either.
The 30-year-old Moller, who has played 82 times for Germany, said he wanted to continue his international career.
"I have asked Berti Vogts not to count me out." he said.
Hassler, 32 and with 97 caps, was more vague about his plans, saying he would be available for selection in case of an emergency. "I don't want to stay in the way of the reconstruction of the national team," he said.
Vogts has made a bold move by recalling Stefan Effenberg, the controversial Bayern midfielder, who has not played for Germany since being kicked out of the team for making an obscene gesture to fans at the 1994 World Cup in the United States.
Marseilles scored five second half goals to complete an astonishing 5-4 victory over Montpellier on Saturday and in doing so went to the top of the French league. At half-time, trailing 4-0, the home side were jeered off the pitch but left the Velodrome as heroes after the fairytale turnaround.
Laurent Blanc, the French World Cup defender, scored an injury-time penalty to complete the second half revival which was sparked by Christophe Dugarry.
He laid on Marseilles' first goal for Florian Maurice then headed two more within nine minutes before Eric Roy's 83rd-minute equaliser.
Montpellier scored four goals, with Ibrahima Bakayoko scoring twice, in a 19-minute nightmare first half spell for Marseilles and their young goalkeeper Porato, who was making his debut in front of 60,000 fans.
Girondins Bordeaux, the only other team on maximum points, beat Auxerre 1-0 at home and lie second on goal difference. Monaco, leaders at the start of the day, were held 0-0 at Toulouse.