Tigres went through 3-1 on aggregate after Saturday’s win, having beaten Chiapas 2-1 at home in Wednesday’s first leg of the quarter-final.
Former Olympique Marseille striker Gignac took a layoff from former Brazil striker Rafael Sobis and volleyed a rising shot into the top far corner in the 21st minute for his 12th goal in 16 league matches.
Chiapas did not live up to their previous form of the season. Before Saturday, they had been unbeaten at home and had qualified for the last eight on the back of a four-match winning run.
Tigres, runners-up in South America's Libertadores Cup in August, will meet record 12-times champions America in the semi-finals.
The Eagles lost 2-1 at Leon on Saturday but went through 5-3 on aggregate following a 4-1 first-leg win at the Azteca.
In Sunday’s quarter-finals, Veracruz visit UNAM Pumas in Mexico City with a 1-0 lead from Thursday's first leg while Toluca are at home to Puebla with the sides level at 2-2.
(Reporting by Carlos Calvo; Writing by Rex Gowar; Editing by Clare Fallon)
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