The England skipper’s 84th-minute spot-kick was held by Alyssa Naeher, shortly before Houghton’s fellow centre-back Millie Bright was sent off for a second bookable offence, as the Lionesses exited at the last-four stage for a third major tournament in a row.
Winger Christen Press and striker Alex Morgan scored with headers either side of Ellen White’s instinctive equaliser as the USA took a deserved 2-1 lead in a frenetic first half.
A spirited Lionesses side improved after the break and White thought she had equalised with a low strike from Jill Scott’s flicked through ball, only to be found to be marginally offside on a video assistant referee (VAR) review.
White was then clipped in the area and Phil Neville’s side was awarded a penalty after another VAR review.
But Houghton could not convert from the spot and the wait for a senior England side to reach a first global final since 1966 goes on.
The USA, who was backed by the majority of the 53,512 crowds in a gripped Stade de Lyon, are through to their third consecutive World Cup final and will now bid for a record fourth title when they face either Sweden or European champions the Netherlands on Sunday.