Croatian Cilic beat the 2010 runner-up in straight sets, two of which went to tie-breaks in a three-hour encounter.
The tone for a tight match was set in the opening two games, both of which went to deuce on four occasions, but, as he did throughout the contest, Cilic came out on top when it mattered and broke in the second game.
Berdych gained a break back when 4-2 down as the first set went to a tie-break, which Cilic won 7-5.
Three breaks were exchanged at the beginning of the second, with two going in favour of Cilic, and the 26th seed did not give Berdych a way back into the set as he closed it out by a 6-4 scoreline.
Both men held firm on serve in the third, with Berdych preventing Cilic the chance to serve for the match when he saved four break points in the 11th game, but it was only a temporary reprieve for the sixth seed.
Cilic recovered from 3-1 down in the breaker to claim a 7-6(5) 6-4 7-6(6) victory, and a notable scalp at SW19.