The third of the Spurs trio, Tom Huddlestone, missed out through suspension after being sent off in the last group game against Serbia on Sunday.
England led 1-0 until the last minute at Heerenveen's Abe Lenstra Stadion when Maceo Rigters' overhead kick took the game into extra time.
By then, England were effectively down to nine men as, having already made three substitutions, Manchester City's Nedum Onuoha had to go off injured and Newcastle's Steven Taylor was limping badly, he bravely carried on.
A marathon penalty shoot-out eventually fell Holland's way 13-12.
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Ben Alnwick and Wayne Routledge were unused substitutes as England lost out on penalties against Holland in the semi-finals of the European U21 Championships on Wednesday night.