Pullman offered the right to name a character in his new book as a lot in the Authors For Grenfell Tower auction, which raised money for victims.
Teacher James Clements had originally bid £1,500 to name the character after his ex-pupil Nur Huda El-Wahab, 15.
Organisers say 448 people eventually added bids to his to secure the lot.
Mr Clements said he used to teach Nur Huda, who lived on the 21st floor of the west London tower block, where 79 people are feared to have died in the fire on 14 June.
Reacting to the news, Mr Clements said he had made a "speculative bid" to win the lot and that "what has happened since has been truly amazing".
"A huge thanks to everyone who has championed, shared or contributed to our team total," he tweeted.
He also praised Pullman for "offering such a wonderful prize and being such a gentleman throughout".
Pullman - best known for his fantasy trilogy His Dark Materials - said it was "great news", adding: "I look forward to writing about Nur."
He said her character would feature in the second novel of Pullman's Book of Dust series to be published next year.
The first part in the series, La Belle Sauvage, is published in October.
Pullman said he could not guarantee whether the character would be "good, bad, beautiful or otherwise", but it would be "a speaking role with a part to play in the plot".
One of the organisers of the auction, Molly Ker Hawn, praised bidders who won the name for Nur Huda, saying: "I love every one of you."
Organisers said more than £150,000 had been pledged in total in the auction when bidding closed.
More than 700 lots featured on the charity site, including signed books from authors Malorie Blackman and Caitlin Moran, and afternoon tea and a book reading with TV personality and children's author David Walliams at Claridges.
Money from the Authors For Grenfell Tower site will go to the British Red Cross London Fire Relief Fund.
A character in a new Philip Pullman book is to be named after a teenager feared dead in the Grenfell Tower fire, following an auction bid of £32,400.