The Blue Samurai drew level with the Group B leaders on 10 points after a tempestuous clash in Saitama.
The Blue Samurai drew level with the Group B leaders on 10 points after a tempestuous clash in Saitama, where Kiyotake's spot kick and a Genki Haraguchi effort eased the pressure on under-fire coach Vahid Halilhodzic.
Saudi Arabia pulled a late goal back through Omar Othman but it was not enough for the visitors to rescue a draw.
"Credit to the players for beating a good Saudi team," said Halilhodzic, whose future has been plunged into doubt after a poor run of form during the Asian qualifying campaign.
"This is a big victory for us but it was a deserved one," added the Franco-Bosnian after his side improved to 10 points from five games, with five remaining.
"We have had to stay strong to come back from some difficult situations and no doubt there will be more to overcome before we get to Russia."
Kiyotake converted on the stroke of half-time after Saudi defender Abdulmalek Al Khaibri was adjudged to have handled, despite replays showing Kiyotake's initial shot had struck him in the chest.
The Saudis protested furiously to referee Muhammad bin Jahari of Singapore and scuffles broke out between the players, which continued as they disappeared down the tunnel at the interval.
Haraguchi effectively killed off Saudi's hopes of pinching a point with a sharp finish after 80 minutes following a deft flick from substitute Shinji Kagawa.
Othman's 90th-minute strike crept across the line in a moment of cruel irony for Japan, who had a similar effort disallowed in a 2-1 defeat to UAE in September.
Saudi's chances of pulling off an improbable escape evaporated when captain Osama Hawsawi saw red for a clumsy challenge in injury time.
Saudi Arabia, who have failed to qualify for the last two World Cups, could have opened a six-point lead over Japan.
"It's difficult to accept losing but we have to be honest and say that Japan deserved to win," said Saudi Arabia coach Bert van Marwijk.
"We have the same points and the group will be cloe."
Australia dropped to third with nine points after drawing 2-2 with Thailand in Bangkok.
Halilhodzic described the Saudis as "specialists in provocation" before the game and also complained Japan had been on the wrong end of dubious penalty decisions against the United Arab Emirates and Australia.
Japan's shock home loss by the Emirates was followed by last month's 1-1 draw with Asian Cup holders Australia in Melbourne, which saw them slip down to third and out of the automatic qualifying spots for Russia.