Jenkins has not played since January, and is battling to overcome a calf injury.
Wales' World Cup plans have already been affected by the losses of hooker Matthew Rees (neck), centre Gavin Henson (wrist) and wing Morgan Stoddart (broken leg).
Gatland will announce a 30-man squad for the tournament next Monday, and while Cardiff Blues loosehead Jenkins is likely to be included, he is currently not available for match-day selection.
"Unfortunately, Gethin's calf is still not 100 per cent, and that is a concern for us," said Gatland, after naming his team for next Saturday's final warm-up fixture against Argentina.
"We have had him rescanned, and there is some damage in the calf. I would say it probably rules him out of contention for the South Africa game if selected (for the squad).
"He is as frustrated as anyone. He has worked really hard, he just hasn't been able to get himself right.
"We know what a quality player he is, and the hope is he will show signs of improvement and maybe we will be able to consider him for other games in the World Cup."
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