Defending champions the Reds led 12-8 at half-time on the back of four Mike Harris penalties but fell behind in the 67th minute when man-of-the-match Sarel Pretorius darted over for the Waratahs' second try of the contest.
But the visitors had the final say when Brendan McKibbin failed to find touch in the final minute, allowing the Reds to counter attack.
The Reds shifted the ball the width of the field and Shipperley broke free as the siren sounded and beat a desperate last-ditch attempted tackle from Bernard Foley to complete his 60-metre run to the tryline in front of 32,071 stunned fans.
Harris slotted the conversion to make it a perfect seven-from-seven with the boot after landing six penalties in a solid performance.
It was a heart-breaking end for the Waratahs who outscored their opponents two tries to one but had to settle for a single bonus point for finishing within seven points.
Stand-in skipper Daniel Halangahu landed three penalties and a conversion while number eight Wycliff Palu scored a first-half try in an impressive return from injury.
The Waratahs hit the front with a long-range penalty from Daniel Halangahu, but Harris levelled things up in the seventh minute from directly in front.
The contest had all the usual spice of a NSW-Queensland grudge match, Palu penalised for angrily shoving former team-mate Beau Robinson's head into the turf after becoming entangled in the 13th minute.
Harris added two more penalties in the 22nd and 33rd minutes to give the visitors a 9-3 advantage before the Waratahs scored their first try from an attacking scrum on 38 minutes.
Palu lost control of the ball at the back of the scrum allowing Will Genia to swoop, but the Reds half-back lost possession in a tackle from opposite number Pretorius allowing Palu to fall over the line.
Halangahu was unable to convert from out wide and when Benn Robinson was penalised for a ruck infringement Harris landed his fourth penalty for a four-point half-time lead.
The NSW captain trimmed the difference with a 40m penalty two minutes in but Harris answered from the sideline five minutes later to restore Queensland's four-point buffer.
Waratahs hooker Tatafu Polota-Nau was denied a try two minutes later after the officials ruled Tom Kingston's pass travelled forward to ruin the crowd's celebrations after the hooker out-sprinted the cover defence from 40 metres out.
Momentum stayed with the hosts who again closed within a point via Halangahu's third penalty on the hour.
The Waratahs continued to surge and hit the front when Pretorius darted over from close range after some good lead-up work, with Halangahu converting for a 21-15 lead.
However, Harris hit back off a scrum penalty on 73 minutes before Shipperley's try snatched victory from the jaws of defeat after the siren.