The 210.9km stage was reduced to just 155km, which removed the last two Hors Categorie climbs from the route of the queen stage.
The snow ploughs were out in force towards the end of the stage, but organisers had to concede defeat to the elements, and the lack of a mountain-top finish gave the 10 riders in the early breakaway a chance to grab a stage victory.
And it was Astana's Brajkovic who outpaced Michael Golas (Omega Pharma-Quick Step) and Mickael Cherel (AG2R La Mondiale) in the race for the line.
On a challenging day for the cyclists a number of riders abandoned, including RadioShack-Nissan's Andy Schleck, while Movistar's Alejandro Valverde who did not even start.
Julian Dean and Frantisek Rabon were involved in a pile-up after only five kilometres into the stage and also withdrew.
It is expected that the stage will not count towards the general classification.
The seven-stage race resumes tomorrow, with a 199km route from Tremp to Asco.