Joe Marler will win his 50th cap and will lead the team out of the tunnel in what is the 124th edition of the Calcutta Cup.
England host Scotland in the RBS 6 Nations on Saturday March 11, kick off 1600 GMT at Twickenham, London and is screened live on ITV.
Vunipola has played just 72 minutes for Saracens since suffering a knee injury in November and despite returning to the England camp this week, Jones has opted against naming him in the starting XV.
It was widely expected that Vunipola would be drafted straight back into the starting line-up but will have to settle for a place on the bench for now, with Nathan Hughes regaining his spot in the back row.
England: Brown; Nowell, Joseph, Farrell, Daly; Ford, Youngs; Hughes, Haskell, Itoje, Lawes, Launchbury, Cole, Hartley (capt), Marler.
Scotland: Hogg (Glasgow); Seymour (Glasgow), Jones (Stormers), Dunbar (Glasgow), Visser (Harlequins), Russell (Glasgow), Price (Glasgow); Reid (Glasgow), Brown (Glasgow), Fagerson (Glasgow), R Gray (Toulouse), J Gray (Glasgow), Barclay (Scarlets, capt), Watson (Edinburgh), Wilson (Glasgow).More news: Economic Snapshot: Private sector employment adds record-high jobs in February
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When it was pointed out that his answers could be construed as ambiguous, Jones added: "Yeah, but I think he'll be all right, is that okay?"
However, they will arrive in good heart this time having won two games and delivered some exciting performances, and would love nothing more than to be the team that brings England's winning run to an end one short of the record. He's one of our best players, but he's not ready to start yet.
Jones' men are only two wins away from equalling New Zealand's incredible record of 18 wins on the bounce and the return of Vunipola might prove to be a massive boost in their mission to make that record their own.
After a fortnight of nothing but praise, the last thing Owen Farrell needed was an injury..
Should Wales beat Ireland in Cardiff on Friday then England can secure the Six Nations title with a game to spare by beating the Scots.
Scotland find themselves in the unusual position of chasing down a Triple Crown heading into the penultimate round of Six Nations fixtures this weekend.