American Lyles, who had been struggling with an ankle injury, began his season in earnest last week with victory over 200m in Monaco and was in confident mood ahead of Saturday's shorter clash.
However, Seville, who was so impressive through the rounds at last year's Olympics before finishing last in the final, roared into a two-metre lead after 20 metres and was never threatened as he came home clear.
Lyles produced his usual late surge but it was enough only for second in 10.00, with Britain's Zharnel Hughes third in 10.02.