Keen had been due to compete in the championship decider alongside Cottingham in 2 Seas's #4 Mercedes-AMG GT3, replacing regular driver Jonny Adam who is unable to race at Donington due to a European Le Mans Series commitment.
Together, Adam and Cottingham lead the British GT3 standings by 13 points having taken three wins and a further two podiums this season.
But Aston Martin factory driver Adam, who already has four British GT titles to his name, will be absent despite attempts being made for him to race at the season finale.
Keen, who currently shares the British GT wins record with Adam, had previously been announced as racing in the Scot's place earlier this season.
He has already competed in the sister 2 Seas machine in Portimao alongside reigning champion Ian Loggie, filling in for Mercedes factory driver Jules Gounon, and had tested with the team and Cottingham at Donington earlier this month.
But the Anglo-Bahraini squad announced on Wednesday that Ellis, a Mercedes factory driver since 2021, would instead fill the role alongside Cottingham.
Ellis has represented the manufacturer in the GT World Challenge Europe and America series, DTM, IMSA, GT Masters and Intercontinental GT Challenge, but has never raced in British GT.
Cottingham said: "I couldn’t have asked for a better team-mate at the start of the season than Jonny, who we knew would be missing two rounds, and we were fortunate that it ended up being one after the rescheduling of one of the rounds that clashed.
"Regrettably now, for us, he has to honour his commitments, which we always knew to be the case.
"With the title going down to the wire, Mercedes-AMG have reached out to provide one of their drivers for the final round, to give us the best possible opportunity to push for the best possible result at Donington to challenge for the title.
"They want to make sure everything possible is done from their side, with no stone left unturned, so it’s exciting to be working with Philip for the weekend, and I’m grateful to Mercedes-AMG for their support, which underlines how seriously they see the British GT championship."
Cottingham currently holds a 13-point buffer over Century Motorsport BMW M4 drivers Darren Leung and Dan Harper ahead of the season finale on 22 October.
Despite not racing, it would still be possible for Adam to seal the title alongside Cottingham, if Leung/Harper fail to overturn the 13-point deficit and Cottingham does not add to his tally.
