Four-time world champion Higgins hit a break of 131 to go 2-0 ahead and Allen stayed in touch at 4-2 before the Scotsman pulled clear.
Higgins added a 123 break as he eased through to a decider against Stuart Bingham, who beat Shaun Murphy 9-8.
Allen defeated world number one Mark Selby 6-5 in the quarter-finals.
Antrim player Mark Allen is out of the China Championship after suffering a 9-3 semi-final defeat against John Higgins in Guangzhou on Friday.