The 27-year-old wing - formerly a Sevens specialist who won Olympic silver in 2016 - has a minor muscle strain and has been replaced by Anthony Watson.
McConnochie, who only switched to the XV format last year, missed last Sunday's 33-19 victory over Wales at Twickenham due to a hip problem.
"Ruaridh McConnochie has been withdrawn from the squad today due to a minor muscle strain and will be replaced on the right wing by Anthony Watson," the RFU said in a statement.
Jones had said on Friday that McConnochie's injury was a different one to the previous week.
Jones will still have two chances to blood McConnochie before their World Cup opener, against Tonga in Japan on September 22, with warm-up Tests against Ireland next Saturday at Twickenham and then Italy on September 6 in Newcastle.
15 Liam Williams, 14 George North, 13 Jonathan Davies , 12 Hadleigh Parkes, 11 Josh Adams, 10 Dan Biggar, 9 Gareth Davies, 8 Ross Moriarty, 7 James Davies, 6 Aaron Wainwright, 5 Alun Wyn Jones (captain), 4 Jake Ball, 3 Tomas Francis, 2 Ken Owens, 1 Nicky Smith
Substitutes: 16 Elliot Dee, 17 Wyn Jones, 18 Dillon Lewis, 19 Aaron Shingler, 20 Josh Navidi, 21 Aled Davies, 22 Jarrod Evans, 23 Owen Watkin
15 Elliot Daly, 14 Anthony Watson, 13 Jonathan Joseph, 12 Piers Francis, 11 Joe Cokanasiga, 10 George Ford (captain), 9 Willi Heinz, 8 Billy Vunipola, 7 Lewis Ludlam, 6 Courtney Lawes, 5 Maro Itoje, 4 Joe Launchbury, 3 Dan Cole, 2 Luke Cowan-Dickie, 1 Ellis Genge
Substitutes: 16 Jamie George, 17 Joe Marler, 18 Kyle Sinckler, 19 George Kruis, 20 Jack Singleton 21 Ben Youngs, 22 Owen Farrell, 23 Manu Tuilagi