McClaren's 4-3-3 formation at the start had turned into a 4-5-1 as Crouch was left painfully isolated in attack and his flick-ons were easily dealt with by the Croatians.
Portsmouth, who have lost key players Peter Crouch, Jermain Defoe, Glen Johnson and Sylvain Distin this summer, made a bright start but City soon got into their stride.
Crouch has now scored 18 goals in 35 England appearances and, although he said he did not expect to start in England's next game against Brazil in a friendly, he hopes to have given Capello a selection dilemma.