Daniel Arreola put the Mexican side ahead after 36 minutes and fellow midfielder Christian Bermudez made sure in the 69th of the quarter-final at Zayed Sports City stadium where the 7,222 crowd was less than a sixth of capacity.
Atlante substitute Lucas Silva added a third in stoppage time after Oceania champions Auckland had come close twice in the second half with efforts by Chad Coombes and Adam McGeorge saved by Atlante's captain and goalkeeper Federico Vilar.
Atlante will play Barcelona next Wednesday, the day after the first semi-final between Asian champions Pohang Steelers of South Korea and South America's Estudiantes. Auckland will play for fifth place against Africa's TP Mazembe in Wednesday's double bill.
Auckland had nine men behind the ball for long spells in the first half and often the only player in the Atlante half was Argentine Vilar.
The New Zealand amateurs, who became more adventurous after the interval, managed their first shot at goal from former South Korea midfielder Lee Ki-hyung in the 34th minute.
ARREOLA OPENER
Their massed defence held out until the 36th when a mis-kick by midfielder McGeorge attempting to clear from a corner gave Arreola a free shot at goal to put the Mexican side ahead.
"We showed great maturity, we had to be very patient. We're not used to playing a team who get all 11 behind the ball," said Atlante's Argentine midfielder Santiago Solari.
"It's a life or death match and you can't afford to make any mistakes. If you make a mistake the story could be completely different."
Striker Rafael Marquez almost added a second from another corner less than a minute later, his sharp header to the top corner being headed out on the line by left back Ian Hogg.
"It was unfortunate we conceded the first goal on an error...could have been 1-1," Auckland coach Paul Posa said after two close misses for his team early in the second half.
Right back Coombes, who scored a fine second goal in Auckland's 2-0 win over home team Al Ahli in the inaugural match, shot low from the right and Vilar made a diving save in the 47th minute.
Just past the hour, Atlante survived another scare when defender Miguel Navarro blocked an effort in a goalmouth melee and McGeorge shot from the rebound only for Vilar to save well.
The diminutive Bermudez, nicknamed Hobbit, scored Atlante's second with 21 minutes remaining when he exchanged a one-two with Marquez and shot between keeper Jacob Spoonley's legs.
Marquez missed a sitter in the 75th when he shot wide with only Spoonley to beat and Atlante had other chances before Brazilian Silva added their third in stoppage time.
