CANBERRA, Australia—The nearly three-year search to resolve one of history’s biggest aviation mysteries ended on Tuesday the same way it began: with the barest of clues over what happened to missing Malaysia Airlines Flight 370.

The Australian government, which led the search with help from China and Malaysia, said the chances of finding the airliner have grown increasingly unlikely amid a lack of credible new evidence. It stopped the hunt and withdrew the last search vessel, the Fugro Equator, which spent its final day in...