Only the top eight teams on that date will compete in the tournament.
As well as Pakistan, Australia, India, South Africa, New Zealand, Sri Lanka and Bangladesh will join hosts England.
Bangladesh, who were last involved in the event in 2006, made sure of their place by beating South Africa in July.
The Windies, who won the Champions Trophy in 2004, suspended coach Phil Simmons on Monday for criticising selectors.
It is the first time they have missed out on a Champions Trophy, World Cup or T20 World Cup tournament.
At the World Cup earlier this year, they were thrashed by New Zealand in the quarter-finals, while Pakistan, India, England and South Africa have all beaten them in ODI series over the past two years.
The next cut-off date for teams is 30 September 2017 – when the top eight one-day sides will earn automatic entry to the 2019 World Cup, which will also take place in the UK.