Scott and Kourtney Kardashian are believed to have travelled to New York last week to attend the funeral. Bonnie lived on Long Island, New York, along with her husband Jeff, where they raised only child Scott.
"Scott and Kourtney travelled from Los Angeles to Long Island for Bonnie's funeral," an insider told Radar Online.
"It was a small affair. There was just a handful of people. No other Kardashians beyond Kourtney attended. But the entire family is saddened with the news of Bonnie's passing. They loved her so much."
Scott has been noticeably absent at several recent Kardashian-Jenner family gatherings, including Kanye West's proposal to Kim Kardashian on 21 October.
The 30-year-old didn't attend the family trip to Six Flags Magic Mountain to celebrate Kendall Jenner's 18th birthday on 29 October. And both he and Kourtney were absent from Kris Jenner's birthday celebration this week.
Bonnie and Jeff Disick were featured on a 2011 episode of Kourtney & Kim Take New York, when Kourtney took son Mason to visit his paternal grandparents in the Hamptons with sister Khloé Kardashian.
Kourtney and Scott have been together since 2006. They welcomed Mason in 2009 and their daughter Penelope in July of last year.