Stoke appeared to be closing in on three points when Hermann Hreidarsson's cross-cum-shot deflected off Shawcross's knee to leave Thomas Sorensen helpless.
The contest had been instantly forgettable until Portsmouth took a 75th-minute lead when Niko Kranjcar latched onto David Nugent's pass and slid a low shot past Sorensen.
But Stoke were level three minutes later from a controversial penalty after Glen Johnson was penalised for handball.
The Pompey full-back was booked for his heated protest as he insisted the ball had struck him on his shoulder.
James Beattie waited for the arguments to calm down before slamming his penalty kick into the top right-hand corner of David James' net, with the England goalkeeper diving in the opposite direction.
The noise from the Stoke fans was now close to deafening and the players responded with Beattie poaching his second, and fourth in five games, ten minutes from time.
Andy Wilkinson's far post cross was fired back across goal by Danny Pugh on the half-volley and Beattie was perfectly placed to nod home from point-blank range.
Tony Pulis' men then attempted to shut out the game and looked like doing so until Shawcross' misfortune in the first of four added minutes.
Neither goalkeeper had a shot to save during a low quality first 45 minutes, although Stoke's power game just about gave them the edge.
There were numerous scrambles in the Portsmouth penalty area, but Sol Campbell and Sylvan Distin, in particular, held firm.
Stoke's best attempt in the first period came through a speculative effort from Liam Lawrence which landed on the top of James' net.
And the visitors had to wait until stoppage time for their only threat when a fine challenge by Abdoulaye Faye denied Peter Crouch a clear strike on goal.
The action improved at the start of the second half and Beattie would have had a clear route to goal if he had managed to control Mamady Sidibe's 47th-minute pass.
But one goal was the most the vast majority of people inside the ground would have expected until the late drama unfolded.