The Trial was ultimately won and lost on the very last section of the event, the man-made hazard comprising huge boulders and giant logs in the town's main street that was used for Saturday's qualification session.
Fajardo arrived here on a total of fifteen, one ahead of Bou, with Cabestany on eighteen and Busto out of contention on twenty-four. With his second victory of the 2018 campaign in his grasp, Fajardo - whose sole TrialGP win up until this season had come in Andorra in 2009 - collected a shock maximum on what was a relatively simple section.
With Bou and Cabestany both nailing inch-perfect rides it meant victory went to Bou from Cabestany by two marks with Fajardo slipping to third on a total of twenty.
"I am very happy with this victory here in Andorra. It's been a tough weekend, with lots of nerves and a lot of pressure, but we've finally won," Bou said.
"Today I felt very good on the bike and my back did not bother me, which is very positive to be able to continue improving like that. This is a very important victory both for the championship and for my morale. To reach victory number ninety-nine is impressive and now we have to work to achieve one hundred victories. I keep saying that this will be a very complicated year for me but we will continue fighting," Bou concluded.
Busto was next on twenty-four before a five-mark gap to his compatriot Adam Raga - TRRS who won in Andorra last year, but never really looked comfortable after a shaky first lap.
Spain's Jorge Casales was the next rider home on a distant forty-six, one mark ahead of British rider James Dabill.
Miquel Gelabert from Spain, Scorpa mounted Frenchman Benoit Bincaz and Britain's Jack Price rounded out the top ten.
The result hands Bou a seven-point lead over Fajardo with Busto a further two points behind as the series approaches the halfway mark.
The 2018 TrialGP series continues in Portugal next weekend.