In a chaotic match where both semi-finalists fumed at the officials, Rublev was defaulted by the chair umpire for unsportsmanlike conduct. Bublik, who clawed his way back from a set down to lead 6-7(4), 7-6(5), 6-5, was awarded the win despite saying that he would be happy to continue the match.
The Russian-born Kazakh, a childhood friend of Rublev, had fought back from 4-2 down in the decider.
Rublev lashed out at the line official at the change of ends after disagreeing with a call.
Another official, who spoke Russian, then confronted Rublev, and appeared to accuse him of swearing at the line judge in Russian, which Rublev denied, but after a lengthy back-and-forth, the 26-year-old was disqualified.
The result meant that Rublev will lose his prize money and ranking points earned at the tournament and that there would be no repeat of last year's title clash where he was beaten by Daniil Medvedev.
The top-seeded Medvedev later lost to fifth-seeded Frenchman Ugo Humbert in the other last-four clash.
"I highly doubt Andrey said something crazy. He's not this kind of guy. But I guess that's the rules. That's what they did, they just follow the procedure," Bublik told reporters.
"There's not much to say. With all due respect, it was a great match and both of us deserved to win. The crowd was there and we could have played one of the greatest matches against each other. It's a pity it ended like this.
"I wish Andrey to get back on track as soon as possible."
Earlier, Rublev was a point away from an early break in the first set, but he raged at an umpiring call and allowed Bublik to hit back and build a 3-0 lead. He then calmed himself and clawed his way back to win the set in a tiebreak.
Having drawn level after a tense second set, Bublik smashed his racket and received a code violation for swearing after he was broken at the start of the next and shouted at the umpire.
But all that paled in comparison to the scenes at the end of the match as Rublev was left to rue a missed chance to reach the final in Dubai for a third straight year.
