The revellers were killed in a stampede at Love Parade on Saturday. More than 300 people were injured in the tragedy, which has been blamed on poor access to the site and the inadequate response of police and security personnel.
Victims were crushed inside a foot tunnel, the only access point to the festival venue, when one end was closed off at 5pm even as thousands of revellers continued to pour in. Eyewitnesses say security staff did little to help those in distress and reported seeing people lying on the ground with "stamp marks on their faces".
The head of the EKD, Nikolaus Schneider, said: "We are devastated by the catastrophe in Duisburg and our thoughts are with those who wanted to enjoy this festival but who lost their lives in such a tragic way."
He said the Church was praying for those mourning the loss of friends and family, the injured, and the police and emergency services.
"We trust in God's promise to us in the Bible, that he is close to the broken-hearted and helps those who are low in spirits," he said.
Love Parade is a techno event that has been held in Germany each year since 1989. At the peak of its popularity in 1999, it amassed a crowd of 1.5 million revellers.
It is believed that 1.4 million people were in Duisburg for the festival on Saturday, despite warnings that the city was too small to cope with such large numbers.
The Catholic Bishop of the Ruhr, Franz-Josef Overbeck called on the Diocese of Bistum Essen, which covers Duisburg, to pray for those who had died.
"It fills me with so much grief to think that so many young people, who wanted a happy and care-free time at the festival, lost their lives," he said.
Pope Benedict XVI said relatives of the victims were in his prayers, while the Lutheran World Federation meeting in Stuttgart remembered the victims in yesterday's morning service.
Spokesman for the EKD in the Rheinland, Jens Peter Iven, said around 50 church counsellors had been deployed in Duisburg to offer comfort and support to traumatised eyewitnesses, festival personnel and members of the emergency services.
Love Parade organiser Rainer Schaller said the festival would never be held again after the deaths.
"The Love Parade was always a peaceful and joyous party that will now forever be overshadowed by these tragic events. The Love Parade is no more," he said.
The tragedy is one of the worst at a music event in the last decade. In June 2000, nine people were killed and 43 injured during a performance by Pearl Jam at the Roskilde rock festival in Denmark. Last year, eleven people were killed during a crush at the Mawazine festival in Rabat, Morocco.