Williams was injured in a heavy tackle by South African centre Francois Steyn and was replaced by Chris Czekaj.
"It looks as though Shane's shoulder has popped out and then popped back in again so we are not sure how long he may need to recover," said Warren Gatland after the game
Wales lost both Jenkins (calf) and Lydiate (ankle) to injuries before the game and both will face a race against time to be fit for their side's final test of the autumn series against New Zealand on Saturday 27 November.
"Dan could be a week or so away from fitness but with Gethin, calf injuries are two or three weeks, maybe a bit longer," added Gatland.
Paul James started in place of Jenkins, with the Blues prop John Yapp called up to bench. In the back-row Andy Powell replaced Dragons flanker Lydiate and Deiniol Jones took Powell's place among the replacements.
Wales welcome Fiji to Cardiff on Friday and the Pacific Islanders began their autumn tour with a 34-12 defeat to France at the weekend, led by Scarlets prop Deacon Manu.