Murray waited out a 3-hour rain delay before prevailing over the fifth-seeded defending champion 5-7, 7-5, 6-3 en route to his fourth overall grass court crown.
Murray showed few signs of rust in his win over Croatia's Cilic, which came after the Scotsman had skipped the French Open with a lower back injury. It marked his third victory of 2013.
His previous London titles came in 2009 and 2011.
Cilic, meanwhile, fell to 1-9 against Murray. He won last year's event in a default when finals opponent David Nalbandian angrily smashed an advertising sign with his racket.
The sign flew into a linesman, causing a gash on his leg.