Resuming at a wobbly 3-37 in reply to WA's 210 at Allan Border Field, Queensland were skittled for 173 on the back of a four-wicket haul from Esterhuysen (4-37 off 13 overs).
WA finished day two at a dominant 0-132 - an overall lead of 169 - with Fanning (82 not out off 134 balls) and Cameron Bancroft (44no off 125 balls) in complete control.
Queensland (34.38 points) entered the penultimate round of the season in second spot, but just marginally ahead of South Australia (33.43 points).
With SA in control of their Shield match against NSW, Queensland's fate will no longer be in their own hands if they lose to WA.
Fanning's current highest first-class score is 99, but he'll have an excellent chance to notch his maiden ton when play resumes on Saturday.
Former Bulls paceman Cameron Gannon helped the visitors stay in the match on Thursday when he claimed three late wickets, including the prized scalps of Marnus Labuschagne (0) and Usman Khawaja (13).
But it was 19-year-old debutant Esterhuysen who was the star of the show on Friday.
The 198cm paceman snared the prized scalp of Matt Renshaw (31 off 94) via a sharp catch at slip from Bancroft.
Esterhuysen sent Jimmy Peirson (1) packing a short time later, before adding another two wickets to his tally as the Bulls crumpled.
A handy 33 from No.10 Jem Ryan helped the Bulls add a vital 38 runs for the final wicket.
But Queensland had no answers for Bancroft and Fanning, with the pair combining for a dominant partnership to put last-placed WA on track for just their second win of the season.
