Phillips' tenure was rumored to be in doubt before the team finished strong and won the NFC East with a 11-5 record. Dallas was ousted in the divisional playoffs, however.
The Cowboys are 33-15 with two division titles in three seasons under Phillips.
Jones, at a season-ending news conference, said, Phillips was a "better head coach than he was three years ago and is a better head coach than we when went into training camp (last summer.)
"We want to build on the foundation we've put in place the past three years."
Jones also said he "saw the team moving in the right direction. It's embracing Wade's leadership as head coach."
Dallas is the third NFL head coaching full-time position for Phillips. He led the Buffalo Bills in 1998-2000, going 29-19, and was coach of the Denver Broncos in 1993-94, finishing 16-16. He also served as interim head coach for New Orleans (0-2) and Buffalo (0-1).