Newton's Principia, first published in 1687, seems like it might be on the late end of that era; by Darwin's time, less than 200 years later, there was presumably no question that On the Origin of Species would be written and published in English. So what was the last one?
That might depend on your definition of 'important', but important works in fields related to ancient history still do get published in Latin occasionally (and if the anecdote is permitted, my faculty still accepts PhD-theses written in Latin). For example, the Corpus Inscriptionum Latinarum, the monumental collection of Latin inscriptions, still gets new volumes that are in Latin. Do you mean primarily in the natural sciences?
Gauss published his Disquisitiones Arithmeticae in 1801.