Hooker Richard Hibbard also misses out after suffering an ankle injury in Wales' win over Argentina.
Cardiff Blues openside Warburton is Wales' youngest World Cup captain.
WALES' WORLD CUP FIXTURES
v South Africa: 11 Sept, Wellington
v Samoa: 18 Sept, Hamilton
v Namibia: 26 Sept, New Plymouth
v Fiji: 02 Oct, Hamilton
His chance to do so comes after hooker Matthew Rees was
with a neck problem.
Warburton's arrival at Test level signalled the beginning of the end of 35-year-old fellow Blue Martyn Williams' international career and he leads Wales into the tournament having led his country only three times.
Williams' only chance of winning a 100th cap would come if Wales need injury cover during the tournament.
Gatland said: "If we had gone 17-13 [forward-backs] on the split we would have taken two sevens.
"We think we've got not a bad seven who's leading the side at the moment.
"We think he's world class and I think Martyn's well aware of that."
Gatland acknowledges having only one openside specialist at his disposal is also something of a risk, but said: "We feel Dan Lydiate can cover there if there was an injury during a match.
"And if Sam gets a serious injury then we are going to have to look at a replacement."
Scarlets fly-half Jones pulled out ahead of Wales'
defeat by England on 6 August at Twickenham with a calf injury.
Preliminary tournament squad members Scott Andrews, Jonathan Thomas, Justin Tipuric, Josh Turnbull and Gareth Delve also also failed to make Gatland's party.
WALES 2011 RUGBY WORLD CUP SQUAD
Ryan Bevington, Adam Jones, Paul James (all Ospreys), Gethin Jenkins (Blues), Craig Mitchell (Exeter),
Huw Bennett (Ospreys), Lloyd Burns (Dragons), Ken Owens (Scarlets).
Luke Charteris (Dragons), Bradley Davies (Blues), Alun Wyn Jones (Ospreys).
Toby Faletau (Dragons), Ryan Jones (Ospreys), Danny Lydiate (Dragons), Andy Powell (Sale Sharks), Sam Warburton (Blues, capt).
Lee Byrne (Clermont Auvergne), Aled Brew (Dragons), Leigh Halfpenny (Blues), George North (Scarlets), Shane Williams (Ospreys).
Jonathan Davies (Scarlets), Jamie Roberts (Blues),Scott Williams (Scarlets).
James Hook (Perpignan), Stephen Jones, Rhys Priestland (both Scarlets),
Tavis Knoyle (Scarlets), Michael Phillips (Bayonne), Lloyd Williams (Blues).
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