Matsuzaka couldn't find his rhythm and left the game after giving up two runs and five hits while striking out three.
"There were good points and bad points," the Red Sox right-hander said. "I'll work hard to get ready for the actual games."
Japan had little trouble with Australia after Matsuzaka left. Seattle star Ichiro Suzuki had two hits, scored twice and drove in a run.
Led by Yomiuri Giants manager Tatsunori Hara, Japan will begin the defense of its WBC title when the tournament begins on March 5 at the Tokyo Dome.
Japan is in Group A with South Korea, Taiwan and China. The top two teams advance to the second round of the 16-nation tournament. The final is scheduled for March 23 at Dodger Stadium in Los Angeles.
Australia is in Group B with Cuba, Mexico and South Africa and will play its preliminary round games in Mexico City.