Oscar Gloukh, a 21-year-old midfielder, scored in the 42nd minute for Salzburg in a game played in front of a crowd of 5,282 at TQL Stadium.
The game was delayed more than an hour after the start of the second half due to lightning in the area.
When play resumed, Pachuca tied the game quickly on a goal by Bryan Gonzalez barely a minute after play resumed.
Pachuca captain Salomon Rondón had a number of chances, including one that hit the edge of the crossbar in the 31st minute, but was ultimately saved by the 18-year-old goalie Christian Zawieschitzky, who was making his Salzburg debut.
The attendance was a major drop compared to Sunday's Bayern-Auckland match on Sunday that drew a crowd of 21,152.
Key moment
When Salzburg substituted Onisiwo for Edmund Baidoo in the second half, and he wound up scoring the winning goal.
Takeaways
With a 2-0 victory, Salzburg rose to the top of Group H heading into its match against Al Hilal on Sunday. Pachuca fell to the bottom ahead of its match against Spanish giants Real Madrid.
What they said
"We will keep working and move forward and do our best to damage control." - Jaime Lozano, CF Pachuca manager.
“We have a young team, but young doesn’t mean inexperience. I think we have a lot of players who’ve played a lot of games, and football has changed a bit. ... I think what’s important for us is that all the agreements wemake beforehand that we stick to them during the game. I think overall, we did that. But of course it was a tough game. They made it difficult for us, but I also think that we showed a lot of character. ... We showed the character that we needed to and found the extra willpower." - Jacob Rasmussen, FC Salzburg defender.
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