The Spaniard had to watch from the pits as title rival Sebastian Vettel ate into his 29-point lead at the top of the drivers' championship at Suzuka.
Alonso spun out of control as the drivers approached the first corner, when it appeared that Raikkonen did not yield to the Ferrari man.
However, the 31-year-old remained optimistic about securing his third world title.
"Well I had no space on the right, I had Button there I think, on the left I had Kimi and I don't understand why Kimi didn't lift off as there was no room out there and it was only the first corner," Alonso told Sky Sports News. "But that is the way it and this time it was us."
"This time I retire, next time maybe it will be Vettel who will retire.
"You never know, this is motorsport. With five races to go it will be like a mini Championship. We will start with the same points and we need to score one more point in the five races than the others so we will try to do that."
Alonso was also forced to retire in the first lap at the Belgian Grand Prix.