The Fujisan in that sentence is not object but theme (or emphasize)
Forget SOV(Subject-Object-Verb) model. It is useful but only a model, after all.
’は’ means "emphasize", which leads to mean "theme" of the sentence.
”ふじさんは見ませんでした。”
means
"Talking about Fujisan (theme), It is that one did not see it"
-> I did not see Fujisan