Khamis, 26, played every game this season and became a key part of the Bulldogs' backline, averaging 6.8 spoils, 4.9 marks and 11 disposals.
The Blues unsuccessfully pursued Khamis in 2024 and tried again this year, before the Bulldogs upped their offer to match Carlton's five-year contract.
"Super happy to be staying in red, white and blue," Khamis said in a statement.
"The factors for me staying were that I wanted to play over 100 games, get the name on the locker. If the name is in gold, that means we have won a premiership, that's the preference.
"We have a great bunch of boys and I love the staff, it is a place I can come to work every day and be happy, be myself.
"I am very grateful to be in the position I am now. To still be here eight years later is special, but I still feel like I have so much more room to grow."
Khamis and his family hail from South Sudan and moved to Australia as refugees when he was a child.
The defender became the Bulldogs' first Next Generation Academy (NGA) draftee in 2018 and is also highly regarded for his community work off the field.
"As a club, we're just so pleased that Buku has decided to remain at our club," Bulldogs football boss Sam Power said.
"He's such a popular member of our football club and has established himself as a key pillar of our back line, showing a great ability to intercept the ball and support his teammates in the air.
"Our commitment to Buku reflects how much we value him - as a player and as a person - with his growing consistency and durability at AFL level an exciting prospect for our club moving forward.
"... We still believe Buku has great growth in his game moving forward and we're excited to see him develop into the future."
The Bulldogs remain firmly in the hunt with Geelong for Port Adelaide superstar Zak Butters.
Gold Coast star Matt Rowell appeared another option but it was reported on Thursday the Brownlow Medallist would remain at the Suns in 2027, when he will become a free agent at season's end.
Elsewhere, Carlton delisted former father-son selections Ben and Lucas Camporeale on Thursday after zero and three AFL games respectively over two years.
After November's draft, the Blues will consider whether to offer the sons of club great Scott Camporeale train-on opportunities.
Carlton have cut nine players in their first off-season under coach Josh Fraser, while Matt Duffy is returning to Ireland.
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