Most of the deciding set was dominated by arguments occurring between Bublik and chair umpire Miriam Bley over the timing of the introduction of new balls.
However, it was world number five Rublev who lost his cool at 6-7(4), 7-6(5), 6-5, yelling towards the official, who claimed the second seed swore at him in Russian.
Rublev insisted he was speaking in English and that he did not use any foul language but the line umpire stuck to his story and the 26-year-old was defaulted from the match.
Bublik tried to convince Bley and ATP supervisor Roland Herfel to continue play but the call was made and the match was over.
The seventh seed now awaits defending champion Daniil Medvedev or French fifth seed Ugo Humbert in the final.
The result also means Bublik has secured his top-20 debut and will become the first Kazakh man to crack the world's top 20 in the history of the ATP rankings when the new standings are released on Monday.
"I would have preferred to lose 7-6 in the third than to win the match like this," said Bublik after the match.
"We could have played one of the greatest matches we played against each other in front of a packed crowd in Dubai. It's a pity it's ended like this."
Up next in the final for the seventh seed is French fifth seed Ugo Humbert, who ended the title defence of Daniil Medvedev with a 7-5, 6-3 win in one hour and 51 minutes.
Rublev found sympathy from Spanish player Alejandro Davidovich Fokina, a quarter-finalist in Dubai, who described the sanction as "shameful".
"Very unfair that they disqualify Rublev without first ensuring that what the line judge understood is correct," the world number 24 wrote on X.
'Shameful'
"That rule should be reviewed and changed. Shameful. We need VAR in tennis."
Rublev fought back from 0-3 down in the first set and played a solid tiebreak to take the lead in 50 minutes, surviving 17 winners off of Bublik's racquet.
The second set followed a similar pattern, with Bublik claiming an early break of serve but failing to maintain his advantage as Rublev forced a tiebreak.
This time though, the big-serving Kazakh snatched the last four points of the breaker to take the semi-final into a decider.
Bublik, who came into the match with an 8-0 record in deciding sets this season, dropped serve in the opening game of the final set, and got into a lengthy argument with Bley about the timing of new balls coming into play.
He also received a code violation for unsportsmanlike conduct for using obscene language in anger after getting broken.
Despite continuing to debate the issue with Bley during changeovers, Bublik managed to break back on a horrendous overhead miss from Rublev, who had seven break point opportunities to extend his lead over his opponent but couldn't convert and the set was suddenly even at four-all.
After Bublik held serve for 6-5, Rublev screamed towards a line judge in anger and soon received his marching orders.
Bublik believes implementing electronic line-calling at all tournaments will help avoid such incidents moving forward.
"We have this proof every week that when the tournament is with electronic line-calling, we don't have this trouble. Players are not getting crazy. It's our passion. We play for this. We live for this. We grew up dreaming to be playing these stadiums," Bublik explained.
"Then some guy who is working for three years as a line judge, staying there deciding something. Then you come up to the situation like this. Is it the fault of Andrey? Maybe. Is it the fault of the umpire? Maybe.
"If we take the umpire out, we cannot take off Andrey. That is the thing. We cannot take off players. Players will be there. It's tennis because of the players, because we are playing this sport, not the opposite way around.
"We can take any umpire away - and that would solve many issues."
Meanwhile, the left-handed Humbert snapped Medvedev’s eight-match winning streak in Dubai to improve to 4-3 head-to-head against top-five opposition and 3-1 overall in clashes against the Russian.
