Honda, who earlier this week missed out on a transfer to AC Milan, entered the game as a half-time substitute and opened the scoring five minutes later, heading home a Yuto Nagatomo cross at the far post.
"In the first half Guatemala were very compact and didn't allow us much space," said Honda. "It wasn't easy, but in the second half we managed to find the gaps in their defence and exploit them."
Japan dominated the first half but failed to make the breakthrough, defender Maya Yoshida firing the best chance over the bar from close range after Guatemala goalkeeper Juan Jose Paredes had fumbled the ball at a 40th-minute corner.
Honda needed little time to make his mark after replacing Hiroshi Kiyotake at the interval, nodding home after Nagatomo had beaten his man to send in a cross.
Kudo then notched his second international goal, bundling the ball home after Makoto Hasebe and Manchester United star Shinji Kagawa had combined to open up the Guatemala defence.
Endo scored Japan's third of the evening after a foul on Honda on the edge of the area, letting fly with a free-kick that struck the defensive wall to wrong-foot Paredes.
"I'm satisfied with the amount of chances we created, but I would have liked to have seen more goals," said Japan coach Alberto Zaccheroni.
Japan next take on Ghana in a friendly on Tuesday in Yokohama.