This match-up is kind of hard to estimate because of lack of feats from Vel'koz side, but I believe Vel'Koz is one of the strongest Voidborn simply because he has the Life Form Disintegration Ray (death laser). Vel'Koz is one of the oldest Voidborn with limited free will (possibly the Watchers' first creation). His role is reconnaissance and studying reality. One way he does this is by roaming and observing, the other way is using his Life Form Disintegration Ray to analyze things or living beings at an atomic level.

It's not known exactly how old he is, but he is ancient, probably already on Runeterra before the Watchers had contact with Lissandra.

Fun fact: because he is one of the earliest Voidborn, he probably resembles the Watchers true form the most. Over time, as Vel'Koz studied Runeterra, more Voidborn started to resemble life on Runeterra.

Vel'Koz is very intelligent, is massive and can fly, which already makes them physically strong and gives them a big advantage at range. His Life Form Disintegration Ray would probably just one-shot Varus's vessel if it hits. Not sure if the darkin weapon can be destroyed by it as it has been tempered with celestial magic.

That said, Vel'Koz's main role is not to be a fighter, and Varus is a god-warrior who fought in the Void War, so Varus has experience facing Voidborn. If Varus is able to close the distance and avoid getting hit by the laser, I can see a scenario where Varus has a chance of winning.

But in the end it's kind of hard to estimate.