The fourth-seeded Russian won in 84 minutes against the top-ranked Nadal, who was uncharacteristically slow and sluggish after having a fever earlier this week.
Moments before the start of the second set, a tired-looking Nadal called for medical assistance and said: "I don't have my game; I feel much more tired."
Davydenko, who beat Nadal in last year's final in Doha, leads the Spaniard 6-4 in head-to-head meetings on the ATP tour. He will look to add to his 20 career titles against second-ranked Roger Federer of Switzerland in Saturday's final.
Two-time champion Federer beat third-seeded Jo-Wilfried Tsonga of France 6-3, 7-6 (2) earlier Friday.
Davydenko beat Federer in the Qatar semifinals last year before going on to win the title against Nadal.
"I have surprised myself by reaching the final," Davydenko said. "I did not expect to do this well. I am happy with my tennis but I can improve (my) fitness."
Davydenko was pleased with his victory but conceded that Nadal was not at the top of his game.
"Normally, he's much tougher and plays stronger," Davydenko said. "I don't mean tennis; I mean physically. He was completely tired running, fighting for points."
Nadal started well and went up 2-1 after a couple of double-handed shots from the baseline in the third game.
Davydenko broke back in the fourth as the top-seeded player started to show signs of fatigue during an error-prone game that included two long returns and a couple of unforced errors.
At 40-all in the eighth game, Davydenko broke Nadal for the second time in the set with two well-placed passing shots from the baseline to go up 5-3 and then held his serve by firing an ace to take the set.
When the match resumed after Nadal received medical assistance, Davydenko kept the pressure on, breaking the Spaniard three times to take a 5-0 lead as Nadal regularly sprayed returns wide. Nadal fought back to secure a break of his own before Davydenko closed out the set 6-2 to win the match.
Federer improved to 22-3 in Doha. He won the title in 2005 and '06.
"I have played good tennis this week so whoever I play against, I am sure it will be a good match," the 16-time Grand Slam champion said. "I have played two finals here so I have the experience."
Although the second-seeded Federer was pushed to a tiebreaker in the second set, he said his early first-set break set the tone for the match.
"It was a crucial service break for me. That set me up nicely for the remainder of the match," the Swiss said. "The second set was more competitive as I was serving really well."
Davydenko knows playing Federer will be a challenge.
"Obviously, he is playing great," the Russian said. "It will be tough. Every day is a different day and let's see how I wake up tomorrow."