“But in stoppage time Eduardo Salvio struck on the counter-attack as the Portuguese side reached the last four.” It sounds (to me) like two independent actions (he strikes, they go through).
You could read it 1) as if Salvio’s strike literary coincided with Portuguese side going through (in fact, it took at least a couple of minutes and a final whistle to see them through). Or 2) was the ‘as’ meant to stress the idea of them going through even without it (the opposite side needed one more to score before his strike)?

It is simply a somewhat loose use of “as” in the sense of two things happening at the same time, or in this case approximately the same time. Journalists are very fond of the word “as”.

I believe it was better being put this way: “Benfica seal their place in the last four as [Rodrigo pulls the ball back from the left and] Eduardo Salvio ghosts in at the back post to fire into the net. Game over.”
–Same scenario, but much cleaner, with Benfica going through at the forefront, don’t you think?

Yes, I agree, it reads better that way round.