The Serb, recent winner of the Australian Open, his 22nd Grand Slam title, also saw his series of twenty consecutive victories come to an end against the world No.7, after 1h35 of play.
Medvedev will face compatriot Andrey Rublev in the final on Saturday, who earlier defeated German Alexander Zverev in straight sets 6-3, 7-5 (11-9), for the first time in six meetings.
"Djoko" returned to Dubai in competition a month after his triumph in Melbourne and a thigh injury.
Impeccable until the semi-finals, with only one set conceded against the Czech Tomas Machac in the first round, the Serb was pushed to his limits by Medvedev in a high-intensity meeting.
"When you play Novak, you have to play your best tennis. I'm happy to have managed to get to his level," said the Russian after the game, author of eight aces on his 27 winning strokes.
After a first set pocketed in 40 minutes, Medvedev then resisted attempts to return his opponent of the day.
"In the second set there were a lot of difficult situations, even though I didn't have a break point against me", he continued, before admitting: "I felt better before the match. that now it's still hard physically", against Djokovic.
On Saturday, Medvedev could afford his third title of the year after Doha and Rotterdam, the 18th of his career, in the event of victory against Rublev, defending champion in Dubai.
For Djokovic, the question now is whether he will be able to take part in the next spring tournaments in Indian Wells (March 8-19) and Miami (March 22-April 2).
On Thursday, he said he was waiting for a decision to be issued before the Indian Wells Masters 1000 draw on Monday (3:00 p.m. local, 11:00 p.m. GMT).
For this, he will have to be allowed to enter American territory without being vaccinated against Covid-19, while the authorities have extended until April the obligation for international visitors to have received the anti-Covid vaccine.
In the event of a ban, he assured that he would withdraw before the draw.
© 2023 AFP