Despite John Barclay's try in the last ten minutes for Scarlets, Wilson's men held out for a 28-22 win to complete a Guinness PRO12 double over the home side.
Warburton put in a man-of-the-match performance and Wilson was full of praise for his flanker.
"I thought he was superb, he caused them huge problems," he said.
"It was a fantastic win. We came here with confidence and a specific game-plan that worked, especially in the first half when the tempo and pace suited us more than them. You don't often come here and say that," said Wilson.
"Fair play to Scarlets, they showed what a good side they are by getting back into the game, but we still showed elements of quality and I was really pleased with our composure at the end when we were down to 14 men to see out the win.
"It is our best win of the season, it is away from home, a tough venue and we haven't won many away from home."
The win keeps Blues in eighth place, just five points off the top six and a place in the Champion's Cup next season, with three rounds to go.
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