Former Cosatu general secretary Zwelinzima Vavi and EFF leader Julius Malema are plotting to overthr.
Chokoe achieved the feat during the South African Football Association's Second Division League national play-offs in Ekurhuleni last week. Baroka FC gained the championship title.
Confirming that the Limpopo side would be retaining Chokoe, club chairman Khurishi Mphahlele said: "We are going to the NFD with Sello.
"We had a meeting where we agreed on a three-year deal, he has been part of the club for a long time and we believe he is the man to take us to the Premier Soccer League.
"We are not in the NFD to stay for long, in fact one season is good enough. Our aim is to see ourselves in the Absa Premiership the following season."
Mphahlele, a Johannesburg-based businessman, added that assistant Matsimela Thoka would also continue in his role in the NFD.
"We are keeping the winning combination because the two gentlemen have done a great job, Limpopo needs more clubs in the PSL," said Mphahlele.
He said they have approached the Polokwane municipality to use the Peter Mokaba Stadium and Oscar Mpetha Stadium in Turfloop.
Mphahlele and Chokoe will hold a meeting later this week to start working on the recruitment of players.
"We will keep the majority of the players who were part of the tried and tested squad.
"At the same time, we will go all over Limpopo in search of new talent. The team belongs to the people of Limpopo, we want them to own it."
Chokoe, who made a name for himself in coaching circles after eliminating Moroka Swallows and Kaizer Chiefs from the Nedbank Chiefs in 2010, said he was pleased to have been offered a deal to continue coaching Baroka FC in the NFD.