Rooney sustained a head injury in training on Saturday following a collision with Jones, who was then substituted during Manchester United's 1-0 defeat to Liverpool at Anfield on Sunday.
Glen Johnson went off injured in the same match, leaving Roy Hodgson, who was there to witness the injuries, with something of an injury crisis ahead of the crucial fixtures.
Daniel Sturridge, who scored the Reds' winner, was struggling with a thigh injury but remains in the squad.
He will join Jack Wilshere, who was substituted before halftime in Arsenal's 1-0 victory against Tottenham with stomach cramps but is expected to report for duty.
Caulker, who moved from Spurs to Cardiff City for 7 million pounds this summer, has represented England's Under-21s on 10 occasions, and scored on his senior debut against Sweden last November.
England currently sits second in UEFA qualifying Group H, two points behind Montenegro but with a game in hand. Montenegro faces a tricky trip to Poland on Friday as Hodgson's men meet Moldova.
The Three Lions then host both Montenegro and Poland at Wembley in the final two qualifying fixtures on Oct. 11 and 15 respectively.
Revised England squad:
Goalkeepers: Joe Hart, John Ruddy, Fraser Forster.
Defenders: Leighton Baines, Gary Cahill, Ashley Cole, Phil Jagielka, Steven Caulker, Chris Smalling, Kyle Walker.
Midfielders: Ross Barkley, Michael Carrick, Tom Cleverley, Steven Gerrard, Frank Lampard, James Milner, Raheem Sterling, Andros Townsend, Theo Walcott, Jack Wilshere.
Forwards: Jermain Defoe, Rickie Lambert, Daniel Sturridge, Danny Welbeck, Ashley Young.