Ninety-three days on from their World Cup semi-final, which the Vatreni won 2-1 in Moscow, the sides played out a far quieter stalemate at an empty ground.
The Three Lions squandered a big chance to win the match through a couple of Marcus Rashford openings early in the second half, while Harry Kane and Eric Dier hit the frame of the goal either side of half time.
A point apiece leaves Spain out in front at the top of Group A4 ahead of Monday's meeting with England in Seville, as they have six points from their first two matches.
England were playing a match behind closed doors for the first time in their history, a run spanning 987 matches, and the lack of noise from the stands was reflected by the events on the field.
England managed just one effort in the opening 45 minutes, coming right at the end when Dier flicked on a corner and hit the far post, which neither Harry Maguire nor Rashford could convert from the rebound due to the awkward bounce.
The Three Lions lacked any sort of creative ideas from open play, though, and their opponents - coming into this match on the back of a 6-0 thrashing at the hands of Spain - did not fare much better.
Croatia should have opened the scoring 37 minutes in through the first half's only real opportunity, only for Andrej Kramaric to hit the ball into the ground when picked out by Perisic's left-sided cross, allowing Jordan Pickford to make the save.
Going into a match with a four-man defence for the first time in a year, which Gareth Southgate hoped would lead to more possession for his side, England offered far more in the early stages of the second period.
Rashford, boasting goals in back-to-back games for his country, dragged a shot wide and Kane sent a header against the crossbar from his first touch of the ball in the final third.
Better chances would fall Rashford's way shortly before the hour mark, but he got his first-time shot all wrong when he only had Dominik Livakovic to beat in the Croatia goal, before being denied by the young keeper on his second cap when attempting to curl it out of reach.
Pickford parried Perisic's low drive to safety up the other end in a more entertaining second half in Rijeka, and Rebic had Pickford a little worried with his well-hit shot that ended inches wide.
Sancho enjoyed a couple of bright moments during his short time on the field, but he could not mark his debut with a telling contribution as the match petered out to its conclusion.
CROATIA (4-2-3-1): Livakovic; Jedvaj, Vida, Lovren, Pivaric; Kovacic (Badelj 73'), Rakitic; Perisic (Pjaca 68'), Modric, Rebic (Livaja 80'); Kramaric
ENGLAND (4-3-3): Pickford; Walker, Stones, Maguire, Chilwell; Dier, Henderson, Barkley; Sterling (Sancho 78'), Kane, Rashford