The Mariners had won each of their first two matches of the season and would have returned to the top with a point.
Instead it is the Wanderers who sit at the summit on seven points from their first four games after their away victory on Tuesday.
Substitute Muller settled a fiery contest in Gosford with seven minutes remaining.
After Joshua Nisbet had hit the crossbar for the hosts, Muller finished calmly from eight yards when fellow substitute Kwame Yeboah's powerful shot deflected into his path.
The Mariners visit champions Sydney FC on Friday, while the new leaders do not play again until their clash with Newcastle Jets on January 29.