Prop Jack Stanley's early try - his second in as many games - had given England a 5-0 lead, but Wales hit back with three penalties to make it 9-5 before England fly-half Theo Brophy Clews clawed one back before the break to make it 9-8.
But Mallinder then stepped up to send his kick between the posts from just short of half way.
Head coach John Fletcher said: "It was almost like a winter's day up north out there - not only was it wet but it was extremely cold. We made mistakes, but that's to be expected in the conditions.
"It's sometimes easier not to have the ball when the weather's like that, and to be honest it could have gone either way.
"We're really pleased to get into the FIRA final though - the lads deserve it. They didn't give up against a strong Welsh defence and got their reward late on."
England will now face Ireland in the final in a repeat of the 2011 and 2012 showdowns after the latter overcame France in their semi-final 24-11 with Sean O'Connor, Jacob Stockdale and Matthew Gilsenan all scoring tries.
Fletcher's side will be bidding for a third straight title after losing to Ireland in 2011 before beating them a year later.
And in the day's other matches, Scotland ran in six tries against Portugal in a 35-11 win while Italy scraped past Georgia 15-13.