Congo won the African play-off final after substitute goalkeeper Timothy Fayulu, sent on late in extra time of a 1-1 draw, made two saves to send his team into the intercontinental play-offs in March.
Late in the shoot-out Chelle became agitated with the Congo coaching staff and had to be restrained by a member of his own staff as he moved towards them.
He was still looking their way when Congo converted the 12th penalty to win the shoot-out 4-3 at which point he again went towards the opposition staff and was again restrained before being led away by a Nigeria colleague.
"The guy of Congo did some voodoo," former Mali international Chelle told reporters. "Every time, every time, every time, so this is why I was a little nervous (of) him."
Asked to explain what happened, Chelle did a gesture of shaking a water bottle.
Nigeria have now failed to qualify for back-to-back World Cups despite star strikers Victor Osimhen and Ademola Lookman being in their career prime years.
Congo last qualified in 1974, when the nation was called Zaire.
They will be joined in the intercontinental play-offs, from which two teams qualify, by Bolivia, New Caledonia, Iraq or the United Arab Emirates and two teams from the north American region CONCACAF, with the remaining teams decided on Tuesday.
