Williams has been struggling with a thigh strain but although he is fit to play, Wales have gambled on resting him ahead of a possible quarter-final against Ireland.
Full-back James Hook (shoulder) and flanker Dan Lydiate (ankle) are also omitted from the side, although Gatland has made seven changes to his line-up following the 81-7 over Namibia.
George North, Rhys Priestland, Jamie Roberts, Mike Phillips, Huw Bennett, Adam Jones and Luke Charteris all come into the side.
Centre Jonathan Davies and lock Alun-Wyn Jones drop to the bench after playing the previous three encounters, with Stephen Jones also having to settle for a place among the replacements.
"Shane might have been available to us if we had pushed him," Gatland said.
"But he has taken a limited part in training this week and we are happy with the back three we have been able to put on the field for this game.
"Alun Wyn Jones and Jonathan Davies are two of the players who have started in all three games so far, and so we have freshened things up a little in the second row and centre, but we have both of them on the bench if we need them."
Victory for Wales - and therefore avenging their 2007 World Cup elimination defeat against Fiji in Nantes - would guarantee them a quarter-final place, although a draw or even just a losing bonus point might also be enough.
Wales: 15 Lee Byrne, 14 George North, 13 Scott Williams, 12 Jamie Roberts, 11 Leigh Halfpenny, 10 Rhys Priestland, 9 Mike Phillips, 8 Toby Faletau, 7 Sam Warburton (c), 6 Ryan Jones, 5 Luke Charteris, 4 Bradley Davies, 3 Adam Jones, 2 Huw Bennett, 1 Gethin Jenkins. Replacements: 16 Lloyd Burns, 17 Paul James, 18 Alun Wyn Jones, 19 Andy Powell, 20 Lloyd Williams, 21 Stephen Jones, 22 Jonathan Davies
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The Barbarians are one of the top invitational rugby sides with a long history and classic rugby jersey.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Lions get ready for their matches with this green training jersey. It's what the players wear. Get in the Gear!
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The Lions are ready to get their Australia tour underway. They arrive in Perth on Monday.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.