The Blues, who won a goal by Joe Cole, advanced, 3-1, on aggregate and will face Tottenham in the final on Feb. 24.
Howard had won the FA Cup with Manchester United in 2004 when it was played at played at Cardiff's Millennium Stadium.
He had no chance on Cole's half-volley in the 69th minute.
"This competition isn't a major competition," Chelsea manager Avram Grant said. "But any game we can win, any trophy we can take, we will do everything it takes."
Blues Salomon Kalou, Michael Essien, Didier Drogba and John Obi Mikel are at the African Nations Cup. Midfielders Frank Lampard and Michael Ballack are injured and didn't suit up. Captain John Terry and forward Andriy Shevchenko didn't make the trip.
Jan. 23 in Liverpool
Everton 0 Chelsea 1. Goal: J. Cole 69.
Everton -- Howard, Neville, Jagielka, Lescott, Nuno Valente, Osman, Cahill, Carsley (Anichebe, 70), Arteta, Fernandes (Vaughan, 78), Johnson.
Chelsea -- Cech, Belletti, Carvalho, Alex, Bridge, Makelele, Malouda (A.Cole, 90), Sidwell, J.Cole (Pizarro, 82), Wright-Phillips, Anelka (Ben-Haim, 90).
Referee: Steve Bennett.