The CSKA Moscow midfielder scored a stunning 30-yard free-kick and set up another goal to help the Blue Samurai to a 3-1 victory over Denmark in Rustenburg. It was his second goal of the finals, following his strike in the crucial 1-0 win over Cameroon in the opening game, but he said afterwards: "I'm not happy and I don't know why.
"Before the start of the match, I could recognise the importance of the match and had expected to be really jubilant if we won," he said. "So I'm not sure, but I think it's because we haven't finished the competition."
The victory was only Japan's second on foreign soil - their first, of course, having been the one against the Indomitable Lions - with their only other win having come on home territory in 2002. However, Honda was pleased for the Asian country as a whole, saying they must now kick on and make it count.
"For Japan it's a big win. I'm glad we won but I am not satisfied," he said. "The next game is more important. I want to show the Japanese that nothing is impossible. We have to still go further and step by step we have to go about doing this. There will be challenges, but I believe the team as a whole can succeed here."
Japan only needed a draw at the Royal Bafokeng Stadium, but Honda insisted they had no intention of just playing for a point. "All the instructions come from our coach. Prior to the match, the coach said we shouldn't concentrate on the defence and that we should attack - otherwise we will never be able to win," he said. "That's what the coach told the players to boost our motivation. It was really effective and led to this wonderful result."
Denmark winger Jesper Gronkjaer was gracious in defeat, but felt the disappointment of not progressing even more because of the way their campaign had taken shape.
"We're really disappointed," he said. "We know we are not any big team, but rather one that is hard working and plays collectively. I think before the World Cup we would have been happy if we reached the third game with the opportunity still there to qualify for the next stage. So now that we are here, we are very disappointed."
The former Chelsea midfielder also paid tribute to the Japanese for making the most of their chances. He added: "We thought we had a good chance and I think the first 10 minutes we created a few chances, but that's what the World Cup is about and the big games are about.
"You have to take your chances and we didn't do it and after that you have to say Japan scored two fantastic goals and they did really well. Credit to them, they had some good players. So we're disappointed now, but we'll get over this, I'm sure."