Cricket South Africa (CSA) said the Proteas were "outplayed" by India in the opening match of the ICC Champions Trophy in Cardiff on Thursday.
Opener Shikhar Dhawan bludgeoned his way to a maiden ODI century as a rejuvenated India kicked off their campaign in with a comfortable 26-run victory over South Africa.
Chasing an imposing target of 332, South Africa were all out for 305.
"What must be really worrying for the Proteas must be the fact that they were outfielded by India, probably for the first time ever. This also cost them vital runs," the CSA said in a statement.
The Proteas lost three wickets for six runs off 13 balls that derailed their runs chase at a crucial juncture.
As a result their second group match against Pakistan has become a virtual knock-out fixture.
CSA said the match will also cause both sides to have a tactical re-think.
"It had been assumed that under English conditions seam and swing bowlers would play a dominant role and that specialist Test-quality batsmen would be required at the top of the order.
"That has not been the case either today or in the warm-up matches. India used three spinners against the Proteas and this was a key factor in their victory.
There were several areas where the Proteas came up short apart from the middle-order batting collapse."
Most important of these was the quad muscle injury suffered by Morne Morkel while bowling the 34th over of the innings.
It meant that he could not complete his quota of overs, having been the most impressive seamer on either side until he was injured.
It probably cost the Proteas a good 20 runs as the other three seamers, who struggled with their execution, were very expensive.