James came off with a calf problem after just half an hour in his nation's group stage finale against Senegal – a 1-0 victory which saw the South Americans advance as Group H winners.
The Bayern Munich man will now miss the match entirely and is one of two changes for Colombia, as Jose Pekerman has also benched Andres Uribe, with Wilmar Barrios and Jefferson Lerma coming into the side.
Meanwhile, Alli returns after suffering a thigh strain in the 2-1 win over Tunisia in the group stage opener.
Kane, who has five goals in his two games, will pair with Raheem Sterling up top.
Alli will team with Jesse Lingard, and Jordan Henderson in the midfield, with Kieran Trippier and Ashley Young providing the width.
Kyle Walker, John Stones and Harry Maguire will form the back line in front of Jordan Pickford in goal.
Fabian Delph is not on the bench for the Three Lions as he remains in England awaiting the birth of his third child.
England XI: Pickford; Walker, Stones, Maguire; Trippier, Henderson, Lingard, Alli, Young; Sterling, Kane
Colombia XI: Ospina; Arias, Davinson, Mina, Mojica; Barrios, Sánchez, Lerma; Cuadrado, Quintero; Falcao.