The defeat in just under two hours also settled the final lineup for the eight-man season wrapup, which starts Monday in London. Stanislas Wawrinka and Richard Gasquet gained the last two places as a result of Raonic's loss.
The 22-year-old from Thornhill, Ont., lost against Berdych for the first time. He had beaten the Czech in both of their previous matches, including a September final in Bangkok.
No Canadian has ever reached the year-end event in singles, though Toronto's Daniel Nestor has made multiple appearances in doubles.
"I didn't have any pressure thinking about London," said Raonic, who fired 18 aces and only lost his serve once. "I actually didn't think about it until I stepped off the court, It was not a part of my mental process.
"The two guys who made London deserved it. I had a match point against Gasquet at the U.S. Open, maybe things would be different now if I had won that one. But I can't really say I'm disappointed.
"I see how close I came," said Raonic, who will still gets a handsome payday as an alternate in London, "I know I can improve a lot more."
Raonic battled hard with the sixth-seeded Berdych during a 68-minute opening set, saving five set points while failing to convert on two of his own.
Once the set was done — Berdych put a forehand winner into the corner to claim it — the Czech then broke Raonic to start the second set.
Raonic was forced to play catch-up and failed to get the break back.
"He played well at the important moments, he was fired up," said Raonic.
"The reason I'm not in London is not because of the last few weeks, it's because of the first five to seven months of the year, when I played poorly at one point.
"There's not too much to be disappointed with, I improved a lot at the later stages of the season. I'm trying to focus on the right things and playing in the right way. I'll have opportunities to contend for bigger moments and bigger events."
Raonic ends 2013 with 45 wins and 21 losses, earning titles at San Jose and Bangkok. He was playing this tournament for only the second time and has yet to get past the third round at the Bercy arena.