Davydenko, the fourth seed, beat No. 6 Tommy Robredo of Spain, 6-3, 5-7, 6-2, in their semifinal match.
Hrbaty advanced when 10th-seeded Tommy Haas of Germany retired in the second set because of gastroenteritis. Hrbaty was ahead a 6-4, 1-0.
After splitting the first two sets, Davydenko was dominant in the third. He broke Robredo's serve twice and didn't face a break point in that set.
It was a tough break for Haas, who needed to win the event to claim the last berth in the season-ending Masters Cup in Shanghai. With his loss, the spot will be filled by American James Blake.
Davydenko, who already earned a spot in the Masters Cup, will play in his seventh ATP final of the year Sunday.