Before the lay-off, Phoenix coach Ernie Merrick insisted the break would be good for his men but it's hard to see how it has helped them based on this week.
The Wanderers were without a win from their first 13 games as their Asian Champions League commitments proved too much for them in the early stages of the season.
Wellington started the better of both sides tonight but Rukavytsya put the home side ahead in the 18th minute as the Phoenix were punished for their sloppy marking.
Rukavytsya, who later left the field in the first spell due to a calf complaint, made the best of the small amount of space given to him and smashed the ball home.
The Phoenix regularly put pressure on the defensive-minded Wanderers but the last pass was missing for the visitors. In Wellington's defence, it was hard to deliver a cross that found a teammate as Western Sydney packed the box.
Nathan Burns, who was part of Australia's successful Asian Cup squad, was one of the game's best players as he continually created chances on attack.
He tore up the Wanderers defence with his deft footwork and pace and given the recent speculation has died down over any potential mid-season move, the Phoenix will be happy to retain his services.
He is in the first year of a two-season deal with the Phoenix and there's no guarantee he will see out the contract as someone may swoop for him during the off-season.
As the second half wore on, Wellington pressed and tried to find to an equaliser but they couldn't hit the right notes.
There were penalty appeals and near misses but the Phoenix barely registered a shot on target as they were smothered in to submission by the Wanderers who just seemed happy to set up camp and defend. In the dying stages, Santalab added the second goal, which settled the result.
Wellington's next game is against Melbourne City at the revamped Hutt Rec in Lower Hutt on Saturday.
Western Sydney Wanderers 2 (Nikita Rukavytsya 18, Brendon Santalab 90+1) Wellington Phoenix 0 halftime: 1-0
