Two balls in the field

[Mando]

I just started umpiring several weeks ago. I was working behind the plate and thank God my partner had to make this call. There was a runner on first base and one out. The batter hits a foul ball just over first base and over the fence. I threw in a new ball to the pitcher. A fan throws the ball back to the first baseman. The batter then hits the ball into the outfield, tries to stretch it into a double, and ends up in a run down. The ball is thrown to the first baseman who now ends up with two balls in his glove. He discards one ball and then tags out the runner. My partner calls out the runner and states that since the first baseman dropped the other ball, the runner advanced at his own risk. I personally would have called obstruction and awarded the runner second base. What's the right call?