The 38-year-old's spectacular scissor kick in the 89th minute sent the reigning champions home with an early defeat, marking Barcelona's first opening-day loss since Pep Guardiola's side crumbled to Numancia in August 2008.
Having just come on as a substitute, Aduriz found himself with time and space in the box to turn in Ander Capa's cross.
Luis Suarez could yet join Messi in the treatment room. Shortly after hitting the post with an uncontested shot in the penalty area, the Uruguayan international walked off with a calf issue of his own.
Rafinha replaced Suarez and buzzed around the pitch, but Barcelona struggled to create chances. The visitors registered just one shot on goal to Athletic's five.