Jones' second half curler sent Anfield in ecstasy as the club's youth academy graduates handed Everton an embarrassing derby defeat.
The 18-year-old Liverpool-born midfielder was making only his fifth appearance and his memorable match winner was his first senior goal.
Jones is the youngest goalscorer for Liverpool in a Merseyside derby since Robbie Fowler.
Without a win over their rivals in any competition since 2010 and thrashed 5-2 at Anfield in the Premier League earlier this season, Everton will feel the pain from this defeat against their under-strength neighbours for some while.
Hit by injuries that left him with 12 fit senior outfield players, Liverpool boss Jurgen Klopp had made nine changes, selecting Nat Phillips, 22, and teenage trio Neco Williams, Harvey Elliott and Jones.