The 32-year-old shared a collage of paparazzi images of his only daughter alongside the message: "One of the only things I'm proud of about myself. Happy birthday P."
Scott's melancholy post was like more than 540,000 times.
It came amid reports Scott has been dumped by long-time girlfriend Kourtney Kardashian, the mother of his three children. As well as Penelope, they have sons Mason, five, and seven-month-old Reign.
Kourtney's reported to have ditched Scott after nine years following pictures showing him getting close to another woman in Monte Carlo while she was at home with the kids in LA.
Neither Kourtney nor Scott have confirmed this.
After Scott shared his birthday message to Penelope, scores of fans commented on how sad the post had made them - while others urged Scott to return home and see his family.
Kourtney took Penelope to Disneyland for her birthday, while Scott was thought to be across the country in Florida.
All you need to know about Kourtney Kardashian: