With the last remaining ballots still being counted, analysts expect the Democrat to pull clear of the new President-elect in the popular vote even though she lost the electoral college tally by some margin.
At least four million votes are yet to be counted in the Democrat-leaning state of California. These are a combination of postal votes and ballots cast by people whose voting eligibility could not be verified on the day.
Nate Cohn, an election analyst at the New York Times, estimates that once all votes have been counted, 63.4 million Americans will have voted for Mrs Clinton and 61.2 million for Mr Trump, giving the Democrat a ‘winning’ margin of 1.5 per cent.
That total would be more than the votes received by any other presidential candidate in history except for Mr Obama in 2008 and 2012.
The total number of votes cast is expected to easily exceed the 129 million from 2012.
However, it is not the overall number of votes cast for each candidate that matters in US presidential elections but the number of votes in the electoral college, which sees each state assigned a number of college votes that go to the candidate who wins the public vote in that state.
Mr Trump won the electoral college after unexpectedly taking states such as Michigan and Wisconsin that had previously been part of the Democrat’s “firewall” of safe states.
He finished with 306 electoral college voters to Mrs Clinton’s 232. More than 270 are needed to win the presidency, giving Mr Trump has a comfortable margin.
The nature of the electoral college has led some peope to suggest Ms Clinton could still become president if electors vote against the instructions given to them by the electorate in their state.
There have been 157 of these so-called “faithless electors” throughout history but they have never overturned an election result and it is unlikely to happen this year.
The unusually high number of votes cast for Ms Clinton is partly due to the rising population of the USA, but also appears to undermine suggestions that, compared to previous candidates, she failed to inspire voters.
The sizeable margin by which Ms Clinton looks likely to win the popular vote will also fuel controversy about the fairness of the electoral college system.
Tuesday’s election – the fourth in which a candidate has lost the popular vote and still won the presidency – has prompted renewed calls for the electoral college to be abolished in favour of a pure first-past-the-past system.
One petition demanding the elecotral college is scrapped has attracted more than 700,000 signatures while another has over 300,000.
Mr Trump himself had previously called the electoral college “a disaster for democracy” after mistakenly thinking that Barack Obama had lost the public vote in 2012 but retained the presidency.
One reason the electoral college was created was to ensure no single region of the US could dominate, such as the North out-voting the South along old Civil War lines, for example.