Hooker, reigning world and Olympic champion, failed to register a vault on Saturday and bombed out.
But Isinbayeva looked in great form as she came in at 4.55m, sailing over that height and qualifying with just the one vault.
The 29-year-old two-time Olympic and double world champion is in Daegu seeking revenge.
She failed to record a height in the final stage of the 2009 Berlin world championships and only came fourth in last year's world indoor championships in Doha after spending years dominating the event.
Joining her in Tuesday's final will be defending world champion Anna Rogowska of Poland, American Jennifer Suhr, who enjoys a world lead this season of 4.91m, Poland's world silver medallist Monika Pyrek and 2003 world champion Svetlana Feofanova of Russia.
Isinbayeva sails through qualification
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