Scheckter will kick of Sunday's sprint race at EuroSpeedway in Germany from the 23rd position out of 25 contesttans.
"We tried really hard to overcome some handling and aerodynamic problems with the car and, although we managed to put in some almost respectable times in the last two qualifying sessions, it was just not good enough," Scheckter said.
"Sure, I'm disappointed and I'm sure South Africans are disappointed.
But I'd like to assure my fellow-countrymen that the whole team is pulling together to see what we can do to improve things. We've got all night before tomorrow morning's 15-minute warm-up and we won't be doing too much resting."
Team South Africa CEO Dana Cooper paid tribute to the efforts of the technical team that has been hard at work trying to get the best out of the South African car, which is called Vulindlela.
"The difference between success and failure here is a fine line. We have only to look at how Team USA has improved since Brands Hatch to see how fortunes swing.
"After impressing in free practice, when he was one of the quickest drivers, Scott Speed could only manage 17th in qualifying and was forced to retire during the feature race. Today, he recorded the fastest single qualifying lap and is second on the grid for tomorrow.
"I have complete faith in our team and am sure they will come back with a roar. With the backing of all South Africans, our national motor racing team will make our country proud."
Nicolas Lapierre of France claimed his first A1GP pole position for the sprint race.
A late scramble among the top contenders in the dying minutes of the final 15-minute qualifying session saw USA's Speed move up into second place overall at the expense of Brazil's Piquet after recording the fastest lap of qualifying at 1 min 32.622 sec.
Great Britain was fourth behind Brazil and ahead of Germany (fifth), Switzerland (sixth), Italy (Enrico Toccacelo) seventh, Ireland (Ralph Firman) eighth, Portugal (Alvaro Parente) ninth and Netherlands (former F1 driver Jos Verstappen) 10th.