The host nation delighted the enthusiastic home fans as they battled back after falling behind to Mark Wilmots' goal to claim their first-ever World Cup point.
Yet a late strike by Arsenal's Junichi Inamoto was ruled out, and Troussier said he did not feel his side had received a fair deal from the official.
It's a historic point because its the first point Japan has
got in the World Cup
"Today's referee awarded free-kicks in favour of Belgium," the Frenchman told reporters.
"The referee might have thought that Belgium were the home team.
"I wonder if the decisions were fair. I wonder if the decisions were made in favour of the home side,"
Inamoto, who twisted an turned while holding off the Belgian defence before slotting home his disallowed goal, said he was mystified as to why the goal had been ruled out.
"I don't know why. Please ask the referee about it," he said.
"I don't know which play was called a foul."
A defiant Troussier added that he expected his team to qualify for the second stage.
Takayuki Suzuki and Inamoto scored the goals which helped Japan avoid the indignity of becoming the first host nation to lose its opening game.
"It's a precious point," Troussier said.
"We played to win, with our qualities, with our faults, with our inexperience."
In France 98 Japan scored just once in three games, and the coach said the confidence from this performance would see his team qualify.
Troussier paid tribute to Japan's fans
"All is possible. There are two matches left and we believe (that we can do it)," he said.
"It's a historic point because it's the first point Japan has got in the World Cup.
"We know we're the challengers in this group and we played a very good European team.
"We tried to show our public the cheekiness of our attacking football and showed we lack a bit of precision and experience.
"But I'm satisfied because everything is still possible."
Troussier paid tribute to the way his team responded to Mark Wilmot's opening goal for Belgium.
"The reaction was wonderful. It was the opening game and you might have thought they would have been a bit paralysed when they went behind.
It was such a good match. I was the most excited I've ever been
Japanese Prime Minister Junichiro Koizumi
"But they proved they are mature. They reacted intelligently and we got this result because of our attacking qualities and we were lucky to have a 12th man (the crowd) behind us."
Japan midfielder Hidetoshi Nakata said: "For the first game 2-2 was not so bad but I think we have got more goals in us.
"We are a very young team and I think tonight's draw will help us in the future."
Japanese Prime Minister Junichiro Koizumi praised the Japanese national soccer team for making its World Cup breakthrough.
"It was such a good match. I was the most excited I've ever been," the premier said at his residence after he returned from watching the game at the Saitama Stadium 2002.
Koizumi arrived at the stadium around 1840 local time to watch the second half of the match with Japanese Crown Price Naruhito and Crown Princess Masako, and Belgian Crown Prince Philippe and Princess Mathilde.
"I would have liked to have seen Japan win, but it was the best result considering the performance of both sides," said the premier.