Jones is heading back west after two seasons with the Toronto Argonauts as their defensive co-ordinator, assistant head coach and assistant general manager.
He replaces Kavis Reed, who was fired earlier this month after Edmonton's 4-14 regular season.
“Chris Jones has paid his dues in the Canadian Football League and has earned this opportunity,” Eskimos GM Ed Hervey said in a statement. “His commitment to the league and record of success is impressive.”
Jones, the 20th head coach in Eskimos history, has helped teams to the playoffs in each of his 12 seasons in the CFL. He has coached in seven division finals and made six Grey Cup appearances, winning in 2002 (Montreal), 2008 (Calgary) and 2012 (Toronto).
Jones beat out a pair of Calgary Stampeders coaches for the job in offensive co-ordinator Dave Dickenson and defensive co-ordinator Rick Campbell.
It's believed Hervey wanted a head coach in place for the Ottawa RedBlacks expansion draft on Dec. 16.
Jones has a great reputation for evaluating talent, being detailed as an organizer and as a coach who holds players accountable.
He began his college coaching career as a graduate assistant at Tennessee Tech University in 1995 and spent seven seasons in the NCAA before entering the CFL in 2002 as Montreal's defensive line coach.
Jones served as the Alouettes' defensive co-ordinator from 2003 to 2007 before spending the next three seasons in the same role in Calgary, where the Stampeders later promoted him to assistant head coach/defensive co-ordinator and assistant director of player personnel.
Last January, Jones withdrew his name from the list of candidates for the vacant head coaching position in Montreal to sign a contract extension with Toronto.
"We've started something great here and I think that, with the players and coaches we have in place, there is an opportunity to build on our championship and contend for the Grey Cup every year," he told reporters at the time.
The Argonauts finished the 2013 season with an 11-7 mark and lost 36-24 to Hamilton in the East final.
It was reported Wednesday that Argos special team's co-ordinator Mike O'Shea is the front-runner to become head coach of the Winnipeg Blue Bombers.