Former Wallabies coach Jones was hospitalised on October 15 and diagnosed with a stroke after complaining of a severe headache.
"He is out of intensive care and is now recuperating in the general ward. He will remain hospitalised indefinitely to rest," a Japan Rugby Football Union spokeswoman said.
"The coach initially complained of mild movement impairment to his left side but is now doing fine. He has been conversing normally from the beginning."
The JRFU said Australia native Wisemantel would take charge against the All Blacks on Nov. 2 at a sold-out Prince Chichibunomiya Stadium when the world champions arrive to begin their northern hemisphere tour.
Technical advisor Wisemantel, 42, had stints as assistant coach for the Wallabies and the New South Wales Waratahs, and his playing career included spells with Sydney's Eastwood Rugby Club and rugby league's Parramatta Eels.
Jones has said his team are training to "beat New Zealand", the level of confidence coming after Japan claimed their first win over Six Nations champions Wales in June.
That win over an inexperienced Wales side has led to public interest in the game reaching an unprecedented level, with tickets for the match to be held at the 25,000-seat stadium selling out for the first time.
But while expectations are high in Japan, who will host the 2019 rugby World Cup, previous games against the All Blacks suggest home fans could be in for a disappointment.
The All Blacks recorded an 83-7 win over Japan en route to winning the 2011 World Cup on home soil and beat them by a record 145-17 at the 1995 World Cup.
Japan will pick a full strength squad for the match, which will, even in defeat, provide a valuable chance to check their progress ahead of the 2015 World Cup in England.
Following their encounter with the All Blacks in Tokyo, Japan will travel to Britain to face Scotland at Murrayfield on November 9, Gloucester on November 12 and Russia at Colwyn Bay, Wales on November 15.
They will play Spain in Madrid on November 23 for the final match of the tour.