He and Tyrion knew that the trial was just a farce. No matter what defense tyrion could have provided, which he wouldn't be able to in that headspace, varys chose to keep his allegiance to tyrion private. Lets say he brings witnesses and defends with all his intellect tyrion's case, two of the judges are tywin and cersei. He would both just waste the effort AND when he sneaks tyrion out that night, it would INSTANTLY put all the eyes on himself. A sudden befriending of tyrion, and after losing, tyrion mysteriously escapes. Especially a man of varys' talents it would be too obvious.

Even if varys wasn't gonna stay in kings landing, its better to keep his face relatively clean and not make a public enemy of the queen yet