The A-League doesn't recognise designated Fifa windows and regularly schedules games in those breaks.
Sydney FC had their troubles too as striker Marc Janko - the A-League's leading goal-scorer - was unavailable due to his commitments with Austria.
The first half was a disaster for the Phoenix as they conceded all three goals. It could have been so different as striker Joel Griffiths was through on goal after a minute but he couldn't convert for the home side.
The goals came in odd ways for Sydney but it didn't bother them. Firstly, Jacques Faty, a Senegalese international, bagged his first A-League goal as the defender scored from close range.
Former Phoenix striker Shane Smeltz was next as right back Matthew Ridenton played him onside and Smeltz poached a goal like he so often has in his lengthy career.
The third came via an own goal from Manny Muscat following a goalmouth scramble, which put the Phoenix in deep waters after only 40 minutes.
Wellington coach Ernie Merrick is never one to sit on the fence when the game needs to chased and he removed Ridenton at the break and introduced the attacking Kwabena Appiah to play on the right wing as he made his senior debut for the Phoenix.
Appiah had his moments and is a player of promise but he wasn't able to help spark an unlikely revival for Wellington.
Aside from a bad result for the Phoenix, they will also be without midfielder Albert Riera against the Melbourne Victory next week after he was shown a red card in the second half, following his second yellow.
It became 10 on 10 shortly after as Smeltz was given his marching orders for lashing out at Phoenix defender Ben Sigmund.
Smeltz left the field to chants of: 'Judas' from the Yellow Fever. The crowd was 6236; not bad considering the game clashed with the Cricket World Cup final.
The outing was one to forget for the Phoenix who probably knew they were always going to find life tough with so many players away.
Sydney FC 3 (Jacques Faty 9, Shane Smeltz 28, Manny Muscat 40 og) Wellington Phoenix 0 halftime: 3-0