Honchar beat German Andreas Klöden by 41 seconds to take the 35.4-mile penultimate stage between Le Creusot and Montceau-les-Mines in a time of 1:07.45. Landis finished in third place, 1:11 behind Honchar, who captured his second time trial of the race.
Landis' finish almost guarantees him the Tour de France crown, marking the eighth consecutive year an American has won the Tour.
Landis was in third place entering the stage, 30 seconds behind Spain's Oscar Pereiro. He finished the day 59 seconds ahead of Pereiro.
Klöden's second-place finish in the stage moved him up from fourth to third. Spain's Carlos Sastre dropped from third to fourth.
The race will conclude Sunday with a 95-mile trek ending on the Champs- Elysees in Paris.