The Dutchwoman, a former heptathlete who took the 200m world title in Beijing with the fourth fastest time in history, showed she has finishing speed to pull clear and finish in 22.12 seconds.
Felix, who won the 400 metres in Beijing but did not run the 200 metres due to a scheduling clash, was a further 0.10 seconds back, but did at least have the consolation of winning the season-long Diamond Race and its $40,000 cash prize.
Schippers, 23, said she was delighted to have settled any lingering debate about who is the fastest for now.
"If you can win everything it gives you a good feeling. It's a fine way of ending the season," she said.
Felix said her final 100 metres was lacking, perhaps a result of focussing on the 400 metres for most of the season, but commended Schippers on an incredible year.
"That's a big confidence booster and you expect her to do well," she said.
"I think there's just a lot of new talent in the 200 metres and that's something exciting to have," added Felix, who hopes to compete in both the 200 and 400 metres in Rio.
In the men's sprints, controversial American Justin Gatlin, who has been banned twice for doping, narrowly won the 100 metres in 9.98 seconds, dipping at just the right time ahead of Qatar's Femi Ogunode, who was given the same time.
Gatlin had also agreed to race the 200 metres an hour later after world and Olympic champion Usain Bolt withdrew earlier in the week, citing a need to recharge.
However, after feeling a twinge in his thigh towards the end of the 100 metres, Gatlin too decided his season was at an end, leaving Ogunode to win the 200 metres in an Asian record time of 19.97 seconds.
Unbeaten until the world championships, Gatlin described his season as bittersweet.
"I was poised to go out there (in Beijing) and win. To be able to come away with two (silver) medals though, is sweet," he said.
In another highlight at the Diamond League finale in Brussels, Tunisia's Habiba Ghibri set a season's best time and African record of 9 minutes 5.36 seconds in the 3,000m steeplechase.
(Reporting By Philip Blenkinsop, editing by Pritha Sarkar)
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