Pistorius, who uses carbon fibre prosthetic running blades, finished in 47.28 seconds behind Lebogang Moeng who won in 45.47.
Pistorius, whose time was short of his season best 45.20, never looked in contention after starting slowly and battled to cope with the searing pace set by Moeng on a hot and breezy day.
The 25-year-old Pistorius, running in lane two, seemed to struggle over the last 100 metres and after the race he said he had felt fatigued.
"It was fine until the 300 then I just felt tired," he told Reuters.
"I felt at that point I was second coming into the corner and then I felt like I was at the verge of pushing it into the red. I didn't see the point of really doing that," he added.
Pistorius shrugged off suggestions the race was a stumbling block to his Olympic qualification.
"It's not a train-smash at all. I'm not overjoyed but I'm not prepared to get injured now for a title that doesn't really mean much," he added.
Pistorius beat the Olympic qualifying time of 45.30 in Pretoria last month but he must repeat that performance in an international meeting before June 30 to make the team for the London Games which start in July this year.