Second year Swindon scholar Aaron Oakley started the game with fellow youth team player Louis Thompson coming off the bench in the second half.
Wales lost the game 3-1 in Slovenia but took the lead thanks to an 11th minute penalty from Tom Lawrence of Manchester United, but Sweden got on level terms after 22 minutes.
Sweden took the lead three minutes before the break and added a third in the 48th minute.
In the other game Russia and Slovenia drew 0-0.
The mini-tournament group also includes the hosts Slovenia and Russia. All three Wales matches will be played in Bakovci. The top two sides from the group go forward to the Elite Round of qualifiers in the Spring of 2013.