Iker Guarrotxena and Brendan Hamill came into the starting eleven, replacing Steven Lustica and Besart Berisha.
Lachie Wales led the line, while Tomi Uskok dropped into midfield.
Sydney had the first chance of the match when Trent Buhagiar weaved his way through the United defence, before having his shot saved by Ryan Scott.
United’s first chance came via an Alessandro Diamanti cross, which found Lachie Wales who couldn’t generate enough power on his header to trouble the Sydney goal.
The visitors dominated territory for the first half and created their next best chance just before the break.
Kosta Barabarouses received the ball outside the penalty area before cutting onto his left foot and forcing another strong save from Scott.
United began the second half more brightly than they did the first and almost took the lead.
Iker Guarrotxena latched onto the end of a superb cross but couldn’t direct his open header on target.
The deadlock was finally broken in the 75th minute when Sydney FC was controversially awarded a penalty for a handball.
In his first game since re-signing with the Sky Blues, Adam Le Fondre emphatically converted the spot kick.
It was enough to secure the win for Sydney in cool Ballarat conditions.
What Mark Rudan said
On the performance
"An absolute superhuman effort by my players.
"We've travelled in five different cities across the countries in fourteen days and played five games
"They gave me everything of themselves plus more."
On the penalty decision
"Adam Le Frondre said it to me, he couldn't believe it.
"The reaction is the first thing that you look for... there wasn't much of a reaction from the Sydney FC players or bench.
"For us to continue to be on the wrong side of these decisions is shattering."
Western United will travel to New Zealand to take on Wellington Phoenix on 22 May at Sky Stadium. Kick-off is 2:05pm AEST.