The two sides clashed in the Toyota Cup at the Royal Bafokeng Stadium on Sunday.
Vilakazi scored the only goal of the match to hand Amakhosi the Toyota Cup title and was deservedly named Man of the Match following an outstanding display.
Despite the victory, Da Cruz acknowledged that it was a challenging contest, with Chiefs still in pre-season while Scottland FC are already in the middle of their domestic campaign.
"It was a difficult game because they played two different elevens and have a different physical status than us because they are in season and we are in pre-season. I'm very happy with Vilakazi because he worked a lot defensively, but he was also able to score," Da Cruz told SABC Sport after the match.
The Chiefs coach also commended the team's collective effort and the impact of his substitutes.
"It was a difficult week, but today was a collective win. The players who came on helped those who started, so it's very important to have that mindset within our team," he said.
Winning the Toyota Cup has given Da Cruz an encouraging start in front of the Kaizer Chiefs faithful.
However, the true measure of the team's progress will come next weekend when the Betway Premiership season begins.