Mikkelsen started the afternoon loop with a 13.6-second advantage over Hyundai driver Hayden Paddon and Ogier another three seconds in arrears.
But after completing a VW1-2-3 - the marque's 107th WRC stage top-three lockout - on SS15 behind Jari-Matti Latvala and Ogier, Mikkelsen hit trouble on SS16.
The Norwegian was quicker through the first split than Ogier but dropped 9.2s to his team-mate after suffering a bent clutch pedal that was touching the brake.
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That allowed Ogier - who had jumped Paddon on SS15 - to close to just 2.8s off the rally lead.
He trimmed by another second with the fastest SS17 time before Mikkelsen, who stopped on the road section after SS16 to work on the car, hit back on the second running of the superspecial to close the loop with a two-second margin.
Paddon is keeping it a three-way fight for the final honour of the 2016 WRC season, but the Hyundai driver is 12 seconds behind Mikkelsen with five stages to run on Sunday.
The Hyundai driver was left to lament worse tyre wear than the VWs, saying: "Our tyres are worse than the others I think.
"My tyre management is better than before but still there's more to do. Andreas' problem keeps things tight. We won't give up until the end of the powerstage."
Behind the top three, Thierry Neuville's hold on fourth position became much more secure as Mads Ostberg's challenge faded.
While Neuville lies just half a minute from the rally lead, M-Sport Ford Fiesta driver Ostberg faded over SS15 with set-up issues and dropped behind the third Hyundai of Dani Sordo on SS16.
Esapekka Lappi's WRC2 lead is up to almost four minutes as the Skoda driver closes in on the class title.
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