Well, from your link:
a : government by the people; especially : rule of the majority
b : a government in which the supreme power is vested in the people and exercised by them directly or indirectly through a system of representation usually involving periodically held free elections
While that says "rule of the majority", it also says "especially". So democracy includes things other than rule of the majority. In particular, the very fact of having representatives of any type means that the US is not a direct democracy. It is instead a democratic republic.
It's also worth noting that no one received a majority of the popular vote. Hillary Clinton simply received the largest minority, what is called a plurality of the vote. Trump did win other majorities. For example, he won majorities of states, counties, and electoral college votes. Republicans in general won a majority of the House seats, which in a parliamentary system would have given their choice control anyway.
Beyond that, it's worth noting that Trump won a higher percentage of the vote (45.9%) than Bill Clinton did in 1992 (43.01%), Woodrow Wilson in 1912 (41.8%), and Abraham Lincoln in 1860 (39.8%). Yet the assumption of the question is that the US was a democracy prior to 2016. If not, then the US wasn't a democracy as early as 1824, when Andrew Jackson won a plurality of the popular vote (41.4%) but John Quincy Adams (30.9%) won the presidency.
While rare, Trump's win in the electoral college while failing to win a plurality of the popular vote was not unique. See 2000, 1888, and 1876 for other examples. Grover Cleveland won a plurality of the popular vote three elections in a row without winning a majority once.