Ahly's talismanic striker Mohamed Aboutrika, now in the twilight of his career, drilled home the winner 12 minutes into the second half after starting the game on the bench.
Mexico's Monterrey overpowered South Koreans Ulsan Hyundai 3-1 in the first quarter-final to set up a showdown with English side Chelsea.
African champions Ahly will face Brazil's Corinthians, holders of the Libertadores Cup, in the tournament's first semi-final on Wednesday.
Elsayed Hamdi put the Egyptians ahead in the 15th minute, only for Hisato Sato to equalise with a fierce right-foot drive with snow falling heavily in Toyota.
Hiroshima lost goalkeeper Shusaku Nishikawa after three minutes, taken off on a stretcher with blood stains on his jersey after catching a knee in the face.
Ahly captain Hossam Ghaly was then carried off clutching his knee with conditions worsening to be replaced by Aboutrika. (Reporting by Alastair Himmer; Editing by Justin Palmer)