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"Nobody asked them to sit back and defend," said a dejected Mashaba.
"Players will tend to use their own methods [in defending a lead] and we conceded from a corner kick. Our picking up from the back was not right."
After a 1-1 stalemate with Ivory Coast at the weekend, Baby Bafana were left with a must-win clash in their final Group B match against Egypt on Saturday to cling to their Olympic dream.
The top three teams will qualify for the London Games, while the fourth-placed side will head into a playoff against an Asian country.
The South Africans created a host of chances for a second assurance goal against the Gabonese.
They took the lead after midfielder Mandla Masango struck shortly before the break, but Gabon hit back with a 79th-minute equaliser from lanky substitute forward Diderot Lengoualama.
Baby Bafana had also held a half-time lead against the Ivorians before facing an onslaught in the second half and conceding with seven minutes left on the clock.
Tournament underdogs Gabon had fought hard against the Egyptians in their tournament opener on Sunday, eventually going down 1-0, and they will also carry a slim chance of progressing to the all-important semi-final stage next week.
"Congratulations to Gabon. They did well to get their first point of the tournament," Mashaba said.
He assured that the South Africans would be ready for their crunch match against Egypt.
"We know what to expect and we will plan for them as we have done for the other matches in this tournament."
South Africa is expected to have defender Eric Mathoho (injured) and central midfielder Thami Sangweni (suspended) available for selection.
