Andrea Dovizioso became the second factory Honda rider in three races to suffer mechanical problems, at Phillip Island on Sunday.
Team-mate and former title contender Dani Pedrosa fractured his collarbone when his throttle stuck open at Motegi on October 1.
Dovizioso's Australian exit was less dramatic, but still costly in terms of points, as the Italian retired early in the race due to a steering damper problem.
"It's really a pity that I had to retire today because we had worked hard with team and, after two difficult days of practice, today we had the pace to fight for third position and a podium finish," said Dovizioso, who had finished second at the previous two rounds.
"I made a good start and I was able to recover some positions. On the first lap I did a 1m31.7s without pushing too hard and I was fifth across the line. In the first two laps though I felt the steering was stiff and on lap three this caused me to lose a lot of positions.
"I could control the bike but, although I completed another lap, it was too risky to keep riding and I had to come into the pits. There was a problem at the steering damper mounting - it had moved into an incorrect position, so now we will investigate the causes.
"I'm really disappointed because after two great races in Japan and Malaysia, it was important to make a good race here to fight for third position in the championship. Still, now we will look to get the best results possible in Estoril and Valencia.”
Dovizioso, fifth in the championship, has now dropped 26 points behind third-placed Casey Stoner, with two rounds and 50 points remaining. Stoner won Sunday's race.
Valentino Rossi is 18 points ahead of Dovizioso, while he DNF also looked to have cost Honda a chance of the 2010 Constructors' title. Yamaha is now 39 points clear of Honda.
Pedrosa's tried to return to action in Australia, but withdrew after qualifying.