Alessandro Schopf scored the only goal midway through the first half after good work by Marko Arnautovic and Stanislav Cherchesov's Russian team looked short of quality throughout.
Sergei Ignashevich returned to the starting side after a two-year absence but did little to improve their defensive woes.
Ignashevich became the oldest player to appear for Russia at 38 years and 320 days, surpassing ex-Soviet Union keeper Lev Yashin, who played his last international at 37 years and 267 days.
Russia, who failed to get past the World Cup group stage in 1994, 2002 and 201, are in a relatively weak-looking Group A alongside Saudi Arabia, Uruguay and Egypt.
New-look Japan suffered a 2-0 home defeat by Ghana to leave new coach Nishino with tough decisions to make less than three weeks before their first match in Russia.
The Blue Samurai will open their World Cup Group H campaign against Colombia on June 19. Poland and Senegal are the other teams in their group.
Nishino deployed a new formation with three central defenders, two wing-backs and two inside forwards supporting a lone striker.
However, Ghana captain Thomas Partey scored and debutant Emmanuel Boateng converted a penalty to ensure a miserable night for Japan in front of 64,520 fans at a rain-soaked Nissan Stadium in Yokohama.
"Having not played a game at home in half a year, we absolutely wanted a good game just before the World Cup," Nishino said.
"We gave it a good try, but the result is disappointing. We had chances but couldn't capitalise."
Nishino will name his World Cup squad on Thursday before warm-up games against Switzerland on June 8 and Paraguay four days later.
There was good news for Egypt who are hopeful that forward Mohamed Salah will have recovered from his shoulder injury in time to play in their final World Cup group game.
"The (Egyptian) football association confirms once again ... Salah will be in the World Cup, God willing, and won't be absent for more than three weeks," the Egyptian FA said.
(Reporting by Angel Krasimirov, editing by Ed Osmond)
