The team from DR Congo, who scored in the 21st minute through midfielder Mbenza Bedi, will have an even steeper climb next Tuesday when they meet Internacional of Brazil.
"Each time you pass a peak, the mountain becomes higher," Mazembe's Senegalese coach Lamine N'Diaye told the post-match news conference.
"So, to use a cycling term, this was a first category col. Now we're going to attack a major climb," he said.
"They are a dimension above," he added of Internacional, winners of South America's Libertadores Cup and favourites to reach a final against Inter Milan.
Pachuca's Argentine coach Pablo Marini said his team had dominated for at least an hour but failed to put away their many chances.
Asked if the result was a 'disaster' for Pachuca, Marini said: "Obviously, yes. We knew about Mazembe's strengths but we didn't expect to lose.
"I think the way the match went, we shouldn't have lost. But, unfortunately, we made a mistake with the goal and did not have the calm to put away our chances."
KEEPER'S PRAYER
N'Diaye had no complaints with Japanese referee Yuichi Nishimura, saying: "The cards were well deserved, (the players) were late (in their challenge) to the ball."
Concacaf champions Pachuca almost took the lead in the 19th minute when Argentine midfielder Alejandro Manso's shot from outside the box on the left hit the inside of the far post and crossed the front of goal before spinning out.
In the Congolese side's next attack, Bedi ran into the box on the right onto a fine through ball from forward Mulota Kabangu to beat Colombian goalkeeper Miguel Calero at the near post for the winner.
It was Mazembe's first victory in two appearances in the competition having lost twice in Abu Dhabi a year ago.
Pachuca, in their third appearance in the competition but with only one win in five matches, will play for fifth place against the losers of Saturday's quarter-final.
