The hosts, who also went into the game unbeaten, ultimately won the game thanks to Alessio Pinotti's ninth-minute finish.
The result ended the Under-19s' perfect six-from-six start to the campaign, although they do still remain top of the table with 18 points.
"I can't reproach the boys, they were always very focused and determined out there - they tried to do what they needed to but that finishing touch was always missing," coach Alberto De Rossi said afterwards.
"It's a frustrating loss to take, especially given how it happened. But we have to put games like this in context too. Everyone fears us and as soon as they take the lead they shut up shop."
The final whistle saw rampant celebrations from the SPAL players, clearly delighted at taking a scalp as the 2020-21 season restarted after a months-long intermission.
De Rossi added: "I don't worry about other sides. We need to focus on ourselves and what we can do better. We tried to find ways to break them down but they were able to hold firm."
The side are back in action next Sunday, as they host Torino at Stadio Tre Fontane (12:30 CET).
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