A day earlier, triple jumper Paraskevi Papachristou was withdrawn from the London team for a tweet on Africans in Greece that was slammed as racist, shocking a nation already reeling from a severe financial crisis.
"This is a bad day for Greek sports," Greek Olympic Committee President Spyros Capralos told Greek SKAI radio.
"In these times that we are going through, we need Greek athletes to succeed, people are expecting success. When such a blow comes, it saddens and disappoints everybody."
Chondrokoukis, who was one of Greece's best hopes for a medal in track and field, will undergo a B test to try to prove his innocence after testing positive for banned anabolic steroid Stanozolol, his father and coach said.
"Dimitris will not take part in the Olympic Games, leaving unfulfilled a dream of a lifetime," Kyriakos Chondrokoukis said in a statement.
"I will fight - we will fight - to respond and see exactly what happened. Not only for us as a family, but for the sports fans who have embraced Dimitris with so much love."
Chondrokoukis, 24, won gold at this year's World Indoor Championships in Istanbul with a personal best of 2.33 metres. His personal best outdoors is 2.32.
Stanozolol is designed to mimic the effects of the male sex hormone testosterone.
Capralos told Reuters the Greek Olympic Committee would not tolerate doping.
"We want to get many medals, however we want clean medals," he said.
Chondrokoukis's lawyer told Reuters he would never commit career "suicide" by taking banned substances days before the Olympics.
"How can it be possible that an athlete who is preparing for the Olympic Games, who won the world championship two months ago and who is being tested every week, has taken a substance that is also the most easily detectable in the banned substances' list," said lawyer Yannis Marakakis.
Greeks suffering brutal salary cuts and tax hikes as the country struggles to exit its fifth year of recession were stunned to hear more bad news from an event many hoped would bring them some relief.
"It's shocking what's happening with Greek athletes and it will make Greece look even worse abroad," said Giorgos Mitsos, 71, an art teacher.
The news just a day before the London Games officially open was a stark reminder to many Greeks of the 2004 Olympics they hosted in Athens, the peak of an era of triumph and affluence that vanished in the wake of the debt crisis shaking the euro.
Greeks spent a fortune building venues that are now often unused.
The 2004 Olympic homecoming was marred when two top Greek athletes, sprinters Kostas Kenteris and Katerina Thanou, were banned for avoiding a doping test the night before the Games began.
Greeks pride themselves on having invented the Games in 776 BC as a sports festival to honour the god Zeus in ancient Olympia. The first modern Games were held in a marble stadium in Athens in 1896.
Often decrying the commercialism and doping scandals that have dogged the modern Olympics for decades, some have even proposed hosting the Games permanently in Greece.
Others say it may not be a good idea now.
"Greece cannot become a permanent host for the Games because it lacks the money, the infrastructure and the know-how," said Angeliki Thomopoulou, 31, a computer saleswoman.
"I was so disappointed when I heard about the athletes, I felt ashamed for my country."