Although Leeds had the better of the first half they went into the break level at 1-1, before easing into a second half lead and eventually taking full control of the game.
Pascal Struijk's header from a Barry Douglas free-kick cancelled out the Portuguese side's opener before Pablo Hernandez' spectacular 20-yarder and Helder Costa's neat finish.
Shackleton admitted the Primeira Liga side made life tricky for Leeds in the first half, but the youngster was pleased with how the Leeds performance developed as the game wore on.
They were a decent side, could move the ball well," he said.
"The first half they gave us a few problems, we had to adapt. Second half we dealt with their threat and we went forward much better. Towards the end our fitness really came into play.
"I think we moved the ball quicker and better. We found a way out from the back more often than not. We struggled at times in the first half to get out. We adapted well and in the second half we were much better."
Pre-season results mean little, as Shackleton pointed out, but performance wise he felt today's showing was an improvement on what Leeds served up in their first friendly of the summer at Stoke City in midweek when they were beaten 3-0.
"The performance wasn't good enough at Stoke," he said.
"It wasn't as sharp as we usually are. Today we were much sharper on the ball and moved it how we can move it."
Still only 20, Shackleton has already made himself a first team player under Marcelo Bielsa with 41 Championship appearances under the Peacock's Argentine head coach. He was joined in today's team by youngsters hoping to fully establish themselves in the senior squad. Charlie Creswell came off the bench late on, but Leif Davis, Struijk and Olly Casey started the game alongside their more experienced team-mates and all three had good games.
Shackleton likes what he sees in 19-year-old centre-half Casey.
"Olly is a great player," said the midfielder.
"For such a big, strong lad he's quick but he's also really good on the ball. He's showed that, he's so composed, in areas where you need to be composed, in the middle at the back. He's got all the attributes."