The Diables Rouges looked in control when captain Marc Wilmots gave them the lead in the 57th minute.
But Japan stormed back to equalise within two minutes and then went ahead themselves before Belgium dragged themselves back to square the match through defender Peter van der Heyden.
But they still needed a late let-off to survive, when Japan's Arsenal midfielder Junichi Inamoto had a goal disallowed close to full-time.
A relieved Waseige said: "After losing control of the game to Japan we at least came back.
"We were basically playing an away game. Plus it was the start of the World Cup tournament and we had a positive result."
Waseige was also full of praise for the performance of skipper Wilmots, who will retire from international football after the finals.
"We had a bad spell in the second half but our priceless captain gave us the advantage.
"The problem was that we did not control the game after we had scored.
"Japan suddenly appeared to find more penetration and more depth and we lost all control of the match."
And Waseige added that his team's task was made more difficult by the waves of home support pouring down from the Saitama stands to inspire Japan.
He said: "The crowd was more than a 12th player for the Japanese team. They were exceptional."
After the match it also emerged that Waseige had criticised Genk striker Wesley Sonck ahead of the game.
He had described Sonck, the double player of the year in Belgium, as not being at the "peak of his condition".
Sonck was dropped in favour of Bruges captain for the match but came on and gave a lively performance in the final 20 minutes.
"I don't like his [Waseige's] remarks, I believe that I am working well, but that's life. The coach has made his choice and I must accept it," Sonck had replied.