Australian Daniel Ricciardo took the final point for Toro Rosso, denying Michael Schumacher a top 10 placing in what was the German's final Japanese appearance before retirement at the end of the season.
The safety car was deployed after the first lap with Alonso trudging back to the paddock after his Ferrari went spinning onto the gravel and then back on to the track facing the oncoming cars.
"Five great races coming! If the enemy thinks in the mountains, attack by sea, if they think in the sea, attack by the mountains," the Spaniard's official Twitter feed declared.
Schumacher's team mate Nico Rosberg also retired at the start after a collision with Williams' Brazilian Bruno Senna, who was given a drive-through penalty.
Image: Ferrari driver Fernando Alonso of Spain spins off the track at the start of the Japanese Formula One Grand Prix at the Suzuka Circuit in Suzuka, Japan, Sunday, Oct. 7, 2012.