Prosecutors had alleged the two paintings, which have sat on chairs in the courtroom during the trial, were produced by Siddique in his Collingwood studio and then sold by Gant.
They resembled the late artist’s acclaimed Lavender Bay series and were found to have been painted more than 15 years after his death.
Siddique admitted to making copies but his lawyer said the conservator did not know what happened to them when they left his studio.
Gant’s barrister told the court his client had bought the paintings from Whiteley’s agent in 1988.
Gant sold the painting titled Big Blue Lavender Bay in 2007 for $2.5 million before selling Orange Lavender Bay for $1.1 million two years later.
When suspicions were raised that Orange Lavender Bay was a fake, Gant provided a refund to the buyer and sold it again for $122,000.
Whiteley’s ex-wife Wendy earlier told the trial she knew the paintings were fakes as soon as she saw them.
Ms Whiteley said they lacked the spontaneity, whit and spirit of a genuine Whiteley.
“I don’t know everything he painted, but I certainly know what he didn’t,” she said.
Siddique had to steady himself when the verdict was handed down but Gant did not react. The two men remain on bail and will return to court next week.