Pachuca almost grabbed the lead after 19 minutes when a shot from Argentinean midfielder Alejandro Manso struck the post.
African Champions League winners Mazembe scored the decisive goal two minutes later to book a last-four berth.
Mbeza Beli lashed the ball into the roof of the net from a tight angle after running onto a through pass from Mulota Kabangu.
Mazembe finished with ten men after Zambian midfielder Stoppila Sunzu was sent off for a second bookable offense with nine minutes remaining.
It was Mazembe's first victory in the tournament after they lost twice in Abu Dhabi last year.
They will be looking to make history when they face Brazil's Internacional in the semi final on Tuesday.
Africa's best representative in the Club World Cup was Egyptian giants Ahli, who finished third in the 2006 edition under Portuguese coach Manuel Jose.