Victory, on a two-game losing run, were completely dominant with 18 shots to nine but had three goals chalked off at AAMI Park before seizing control on the scoreboard.
Eight days after a contentious VAR intervention denied Victory a match-winning goal in their loss to Adelaide, Jason Davidson had back-post headers ruled out by VAR for offside and handball respectively in the 13th and 48th minutes.
But Spanish maestro Mata notched three assists as Santos - ruled offside in the 10th minute - struck in the 53rd and 64th minutes, with Keegan Jelacic and Lachlan Jackson scoring in the 79th and 82nd minutes.
Diles was delighted his players kept their heads after the disallowed goals and when asked if that was the best win since he took the reins, initially as interim in December 2024, said: "I think so.
"It's hard to remember two dominant halves like that, where you don't fall off.
"Normally, you can have one outstanding half, and you fall away. Or you don't start well, and then you have a great second half.
"But in terms of 90 minutes that was probably the best one so far, for sure."
Mata has been among the A-League Men's best players and has a league-high seven assists.
"He's not a bad player," Diles joked.
"He's doing very well. We're very happy to have him. You can see he's enjoying his football."
Victory are seventh, five points off leaders Auckland and two points behind fourth-placed Sydney.
Victory striker Nikos Vergos was arguably lucky to only receive a yellow card in first-half injury time for a high elbow to Alex Grant, who had to be substituted with concussion, for Jordan Courtney-Perkins
"When I spoke to (fourth official) Shaun (Evans) on the sideline, he said that he got hit in the neck," Sydney coach Ufuk Talay said.
"But I find that very intriguing, because he's actually concussed."
Victory finally broke through when Mata released Santos, who charged forward then beautifully dinked the ball into the top corner.
Melbourne doubled their lead when Mata found Vergos, who flicked the ball on for Santos to beat two defenders and score.
Sydney thought they had responded in the 67th minute when Piero Quispe took a short corner and the ball went through Joel King's legs before the Peruvian sent it in to Victor Campuzano to score.
But it was chalked off as players cannot touch a corner twice without another player touching it.
Victory punished Sydney 12 minutes later when Davidson picked out Mata, who cut back for Jelacic to fire a rocket into the top corner.
Then, the 37-year-old maestro picked out Jackson to complete the rout with a bullet header.
"What we struggled with today was just the basic fundamentals of being able to control the ball and pass the ball," Talay said.
"Generally, when that happens in a game, it's one or two players, but I think it was basically the whole squad struggled with that today.
"I think it's the third time this season we've had an opportunity to go to top spot. And every time we've had that opportunity, we haven't taken it, which is quite disappointing."
Victory travel to face Central Coast next Sunday while Sydney will hope to bounce back in their home derby against the Wanderers on Saturday.
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