Matthew Etherington's first-half strike put the Potters ahead but Hull were rewarded for their greater endeavour as Olofinjana levelled against his former club and substitute Jan Vennegoor of Hesselink won it in the final minute, moments after Abdoulaye Faye was sent off.
The Potters remain a healthy ninth in the table but Pulis admitted his side were below par.
"We're disappointed," he said. "It is the third time we have led away from home this year and not won the game. We weren't at our best but when Matty scored we were hoping that would take us on."