Jones netted three times late on after Liam Millar's opener and a second-half Joe Hardy double had put the Reds 3-0 up.
Liverpool can only be overtaken as group winners if Wigan Athletic win both of their remaining matches and make up a goal difference of five.
Albie Morgan’s 76th-minute penalty gave the Addicks the point they needed to stay above second-placed Reading on goal difference.
Both teams qualify for the last 16 after moving five points clear of third-placed Colchester United, who have one match left.
See: Charlton report
Second-half goals by Alex Hartridge and Harry Kite earned Exeter City a 2-2 draw with Doncaster Rovers to finish top of Group D.
Doncaster finish a point behind Exeter as both teams progress to the knockout stage.
See: Doncaster report