The Briton, keirin gold medallist from London 2012, was beaten by 33-1 chance Jordaura as she rode Royal Etiquette over one mile and two furlongs.
The 34-year-old's racecourse debut came in a charity event at Newbury in July.
She aims to ride in the Foxhunter Chase at the 2016 Cheltenham Festival.
She retired from cycling in 2012 after adding London gold to the sprint title she won at the Beijing Games in 2008.
Olympic cycling champion Victoria Pendleton finished second on her competitive debut as a jockey in the Betfair Novice Flat Amateur Riders' Handicap at Ripon.