Everton had equalized through Aiyegbeni Yakubu in the 64th minute, nine minutes after the ejection of Chelsea's John Obi Mikel.
Howard had kept the game close by denying Peruvian Claudio Pizarro on a clear opportunity in the first half.
Wright-Phillips's goal came on a shot that curled past a diving Howard and bounced in off the post.
"It's really hard to take," said Everton cosch David Moyes. "Chelsea's movement was fantastic in the first half but we kept at it and I thought we might go on and win it."