The reality TV stars were joined Kardashian matriarch Kris Jenner at the ceremony, which was held in Oakwood Cemetery in Bayshore, New York.
The grieving couple were dressed appropriately in black and attended the memorial without their two children Mason and Penelope.
Scott's father Jeffrey passed away on 3 January, just three months after his mother died.
"The whole family is so devastated and Scott is beside himself," a source told E! news. "Scott is an only child with no remaining family."
No further details of Jeffrey's death have been revealed.
The Keeping Up With The Kardashians star lost his mother Bonnie, aged 63, to cirrhosis of the liver in late October.
Kourtney with Bonnie Disick
At the time of her death, sources close to Scott and Kourtney said that Bonnie's death had brought the couple closer together and had made Scott a "much better father " to Mason, three, and 18-month-old Penelope.
"Scott's been more emotional since his mom died," an insider said. "He's now more dependent on Kourtney. It really affected him. He's staying at home more and being a much better father. Scott has grown up a lot. He's much more responsible."
The father-of-two was raised by his parents in Eastport, New York on Long Island before Scott set off for California in his early twenties.
Jeffrey appeared in a 2011 episode of Kourtney & Kim Take New York, when Kourtney and Scott took young Mason to visit his grandparents in The Hamptons.