Williams had never reached the last four in Tokyo before and needed just over three overs to do so as Bouchard put up a fight 6-3 6-7 (7/4) 6-3.
The veteran American, now ranked 63, beat second seed Victoria Azarenka in the second round, and will next meet former Wimbledon champion Petra Kvitova.
"I'm in the semi-finals - I'm so excited, my first semi-final here in Tokyo after all these years," she said in an on-court interview.
"It's hard to believe it's the first time, but I'm glad it's now.
"But my hopes are to win tomorrow. Hopefully it'll be a win - and in less time, that's my goal."
Kvitova beat Svetlana Kuznetsova 6-4 6-1 after they had both completed rain-affected third-round matches earlier in the day.
Second seed Agnieszka Radwanska fell 6-4 6-4 to Angelique Kerber who will meet Caroline Wozniacki in the last four after the Dane beat Lucie Safarova 2-6 6-3 6-2.