First, Scott McKenna was caught on the ball by Bournemouth forward Rayan and Vinicius Jr skipped past Angus Gunn to score.
Gunn and full-back Nathan Patterson were then caught under a Bruno Guimaraes cross as Vinicius Jr nodded in his and Brazil’s second before half-time.
And Manchester United’s Mateus Cunha made it three after the break on a night where Scotland huffed and puffed, but were ultimately outclassed.
“We lose poor goals at poor times against a team that can punish you with quality,” McGinn told BBC Sport. “We had a few chances but we’ve got to wait now.
“The lads are gutted, we fell short on quality but we gave it absolutely everything. The lads are empty now. It’s unlikely [that we qualify] but we’ll wait and see.
“It’s a bit raw at the minute but we appreciate the support of the fans, we know it’s difficult to be there. Hopefully the journey is not over and if we have to go again, we will go again.”