Thierry Neuville had been quickest for Hyundai on the opening Guanajuato street stage, where Ogier was third.
But the reigning World Rally champion, who is unbeaten in the 2016 WRC season so far, set the pace on both runs of the following Leon superspecial.
That gave Ogier a 1.7-second overall lead from Neuville, though he acknowledged that will mean little when the event gets under way in earnest with some extremely long stages on Friday.
Mexico drops WRC's longest stage for 2017
Ogier's Volkswagen team-mates Jari-Matti Latvala and shakedown pacesetter Andreas Mikkelsen hold third and fourth.
With Mexico among the rounds the PH Sport-run Citroen team is skipping and M-Sport pair Mads Ostberg and Eric Camilli only 11th and 12th for now, the top six is shared between VW and Hyundai.
Dani Sordo, whose i20 required some repairs after an impact with a stone on the afternoon's shakedown, and Hayden Paddon are fifth and sixth.
Ford privateer Lorenzo Bertelli was an impressive second fastest to Neuville on the street stage, but slipped back to seventh after the superspecials.
Follow Rally Mexico as it happens with Autosport Race Centre Live from 3pm UK time on Friday
LEADING POSITIONS AFTER SS3:
No repeat for 50-mile Mexico stage
Penalty costs Sordo Mexico podium
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