It even looked as if Pandev would leave the big stage with a final assist, when Ivan Trichkovski netted from his clever through-ball inside 10 minutes, only for it to be ruled out for offside.
Grant Hanley hobbled off injured as Steve Clarke was forced into a reshuffle, Scott McKenna coming on and being instantly booked, such was the intensity of the Croatian surges forward with Modric pulling the strings.
In many parts, this was a colourless England display after they started on the front foot but the results have been delivered in a manner Southgate and his players would have happily settled for when Euro 2020 got under way.
The kick, awarded after Dutch referee Bjorn Kuipers consulted the pitchside monitor, was the fifth successive penalty Spain have missed and they have failed to score with six of their past nine at European Championships.
They came either side of half-time but were not enough to give Portugal victory as striker Karim Benzema broke a six-year goal drought with France to score twice and ensure Les Bleus topped the group.
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