Howley, much criticised for his selection policy, responded by making eight changes to his starting XV, with Warburton's place going to Justin Tipuric.
The captaincy passes to former skipper Ryan Jones, who is set to lead his country for a record 29th time.
Howley has also brought in centre Ashley Beck, first-five Dan Biggar, halfback Mike Phillips, lock Bradley Davies, hooker Richard Hibbard and prop Paul James.
How they line up
Wales: Leigh Halfpenny, Alex Cuthbert, Ashley Beck, Jamie Roberts, George North, Dan Biggar, Mike Phillips; Toby Faletau, Justin Tipuric, Ryan Jones (c), Ian Evans, Bradley Davies Aaron Jarvis, Richard Hibbard, Paul James. Reserves: Ken Owens, Gethin Jenkins, Scott Andrews, Luke Charteris, Sam Warburton, Tavis Knoyle, Rhys Priestland, Scott Williams.
Samoa: Fa'atoina Autagavaia, Paul Perez, George Pisi, Paul Williams, David Lemi (c), Tusi Pisi, Kahn Fotuali'i; Taiasina Tuifua, Maurie Fa'asavalu, Ofisa Treviranus, Filo Paulo, Daniel Leo, Census Johnston, Ole Avei, Sakaria Taulafo. Reserves: Ti'i Paulo, Viliamu Afatia, James Johnston, Tivaini Fomai, Jeremy Su'a, Jonny Leota, Robert Lilomaiava.