Representatives for the two companies accepted they had met with the other agencies in September 2013 but maintained that any decisions about how to respond to Trade Me's new prices were arrived at independently.
Counsel for Lodge and Monarch said they had decided in advance of the meeting to vendor-fund standard listings upon the introduction of the new fee structure.
Justice Pheroze found that the companies were "part of a consensus giving rise to expectations each would not absorb the cost of Trade Me's proposed per listing fee".
However, "the arrangement or understanding between the defendants did not have the purpose or effect of fixing, controlling, or maintaining ... the price for, or any discount, allowance, rebate, or credit in relation to, real estate sales or advertising services supplied by the defendants in competition with each other", the decision said.
Monarch's lawyer, Mark Anderson, said in a statement that the realty market had been left in an unfair position by facing "massive" price increases while also having a duty to protect the best interests of its vendor clients.
"There was no collusive behaviour for gain, agents and vendors were still free to negotiate on price and, in dismissing the allegations, the court recognised the pro-competitive actions of the market," he said.
"The decision is a common-sense reflection of economic reality where even Trade Me recognised that realtors would have to pass the new price on to consumers."
Close to $20m in penalties have already been imposed on the real estate sector in relation to the commission's investigation.
This includes $9.8m against the head offices of Ray White, Barfoot & Thompson, Harcourts and LJ Hooker collectively.
Bayleys was also previously ordered to pay $2.2m and Property Page Limited, which operates the realestate.co.nz site, $100,000 towards the commission's costs.
Two other Hamilton real estate agencies, Lugton's Limited and Success Realty, were earlier ordered to pay $1m and $900,000, respectively.
Three Manawatu real estate agencies were also been penalised: Manawatu 1994 was ordered to pay $1.25m, Unique Realty $1.25m, Property Brokers$1.45m million and its director Tim Mordaunt $50,000.
The commission alleged the agencies breached the Commerce Act by agreeing a planned industry response to Trade Me's pricing scheme.
It also claimed the parties agreed vendors would have to pay the listing fee to have their property advertised on Trade Me, and the agencies would not commit to any preferential or discounted listing fees with Trade Me.