Leigh Halfpenny scored 22 points at the Millennium Stadium on Sunday and Alex Cuthbert scored his first international try as Wales made it two wins from two to start the tournament.
Halfpenny's first try arrived with Scotland's Nick De Luca in the sin-bin for hauling down Jonathan Davies without the ball, and his second - along with a penalty - after Rory Lamont had also been yellow-carded.
And flanker Lydiate, a key figure in a fine display by the Welsh pack, said: "Yellow cards are always crucial, you've got to be squeaky-clean in this day and age and everybody's got to work on their discipline."
Greig Laidlaw's try cut the deficit - after Scotland debutant Stuart Hogg was denied a score when he was adjudged to have knocked on - and Wales had to hang on a man short in the closing moments after prop Gethin Jenkins was also sin-binned.
But they remain 100% ahead of their clash with England at Twickenham in two weeks and Lydiate said: "Scotland came back into it and it was touch and go, at the end we were under the cosh.
"But we're delighted with the win and we've got to be confident going into that game against England."
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