Warburton suffered a knee injury in April and did not play again until leading the Lions in their unconvincing 13-7 victory over the Provincial Barbarians in the tour opener last Saturday.
Ireland's openside flanker Sean O'Brien has been given the nod for the number seven jersey in place of Warburton and will make his first appearance of the tour, with compatriot Peter O'Mahony named at blindside flanker.
"Sam Warburton had a bit of slight ankle strain after the first game, he just needs a few more days," Gatland told reporters in Christchurch.
Gatland added that flyhalf Dan Biggar, who failed a concussion check in the 22-16 loss to the Auckland Blues on Wednesday, would not be available for six days as he undergoes the team's head injury protocols. Loose forward Ross Moriarty has a back strain but was recovering well.
Gatland had said all 41 members of the squad would get an opportunity to play in the opening three games of the tour before he began to decide on combinations for the first test against the All Blacks on June 24.
While Wednesday's defeat to the Blues was far from ideal, Gatland said the squad was on the right track.
"We came back and if we had ground out the win, it would have been a big positive for us," Gatland added.
To combat the All Blacks-laden pack of the Crusaders, with six of the eight players having test experience, Gatland has given props Tadhg Furlong and Mako Vunipola their first starts of the tour.
England lock George Kruis, who is also making his first start, will partner Wyn Jones in the second row.
Gatland has also gone with what many regard as the Lions' top halfbacks combination in Ireland scrumhalf Conor Murray and England flyhalf Owen Farrell.
The hard-running Ben Te'o, who impressed in the opener against the Barbarians, has been named to join Wales' centre Jonathan Davies in the midfield, with George North getting his first start on the right wing.
The Crusaders, who have won seven Super Rugby titles, are unbeaten in the competition this year.
Lions: 15-Stuart Hogg, 14-George North, 13-Jonathan Davies, 12-Ben Te'o, 11-Liam Williams, 10-Owen Farrell, 9-Conor Murray, 8-Taulupe Faletau, 7-Sean O'Brien, 6-Peter O'Mahony, 5-George Kruis, 4-Alun Wyn Jones (captain), 3-Tadhg Furlong, 2-Jamie George, 1-Mako Vunipola
Replacements: 16-Ken Owens, 17-Jack McGrath, 18-Dan Cole, 19-Maro Itoje, 20-CJ Stander, 21-Rhys Webb, 22-Johnny Sexton, 23-Anthony Watson
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
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