In front of 57,226 fans in Perth on Thursday night, Australia looked disjointed and uninspiring throughout the match before Behich popped up for the winner in what was his first international goal in 13 years.
Riley McGree's angled cut back rolled tantalisingly untouched in the box, and Behich ran back and unleashed a right-foot strike while spinning his body to send the ball flying in for a goal.
The result means the Socceroos (16 points, +8 goal difference) will lock in the second automatic World Cup qualifying spot from their group - barring a crazy big loss to Saudi Arabia in Jeddah next Tuesday.
Saudi Arabia (10 points, -2 goal difference) need to beat lowly Bahrain overnight to stay in the hunt to leapfrog the Socceroos.
Behich, who won the A-League title with Melbourne City last Saturday, rated his goal against Japan as his finest moment in Socceroos colours.
"As soon as it's come off my foot, I felt I hit it pretty nicely," Behich said.
"I actually didn't see the ball hit the net. I just kind of saw the crowd erupt and players start running everywhere.
"That's when I'm like, 'Let's go'. It was a beautiful moment."
Socceroos coach Tony Popovic exploded with emotion on the bench when the goal went in, with a flare set off in the crowd to mark the moment.
"It's a special night," Popovic said.
"The outpouring of emotions when we scored, and obviously after the game - it's a moment I'll always remember.
"We've all played a part in getting us to this point, and we want to go to Saudi Arabia now and really finish the job off."
Thursday's result marked Australia's first win over Japan since 2009.
Japan (20 points) entered the match under no pressure to perform given they had already qualified for the World Cup as the winners of their group.
Regulars such as Kaoru Mitoma, Daizen Maida, Reo Hatate, Takumi Minamino, Ritsu Doan, Junya Ito and Hidemasa Morita didn't even make the trip to Australia, while stars Wataru Endo, Takefusa Kubo and goalkeeper Zion Suzuki were named on the bench.
Japan named three debutants in their starting XI as well as six other players with four or fewer international caps to their name.
Australia looked like they had stage fright in the first half, with basic errors and bad decision-making regularly plaguing them.
Japan enjoyed 70 per cent possession for the half, and they gave the Socceroos a big scare in the 28th minute when Yuito Suzuki surged forward and sent his shot just wide.
A goalkeeping error from Japan in the 48th minute gave Behich a sniff that he wasn't able to take advantage of.
But he made no mistake in the 90th minute, burying his chance to send the crowd into raptures.
