Fifth-seeded Rublev, the 2020 champion at the Gulf tournament, battled to a 7-5, 6-4, 7-6(5) win over Auger-Aliassime, who fired down 21 aces in the two-hour, 47-minute semi-final.
"It took everything. It was super tough today," said Rublev whose most recent final appearance was in Montreal last August.
"I felt like there was not much I can do if he is serving like that. I just needed to be really lucky to break him.
"He was serving well and I was just saying, 'Okay, I cannot do much, this is one of the best servers on Tour. I just need to try to guess and when I have a moment, just go for it'."
Rublev, who was also a runner-up in Doha in 2018, secured victory on Friday on a fourth match point. In his quarter-final dismissal of second seed Alex de Minaur on Thursday, he had needed twice as many.
The Russian won the last of his 16 ATP titles on clay in Madrid in May 2024.
On Saturday, the 27-year-old will tackle British eighth seed Jack Draper for the title.
Draper defeated Carlos Alcaraz's conquerer Jiri Lehecka of the Czech Republic 3-6, 7-6(2), 6-3 on the back of 14 aces to reach his fifth final.
Left-handed Draper will be seeking his third career title but will have to overturn a losing 3-0 head-to-head record to depose the Russian.
The 23-year-old is already assured of attaining the best ranking of his career after this week.
A US Open semi-finalist in 2024, Draper will rise from 16 in the world to 11 if he wins the Qatar title and 12th as runner-up.