The margin did not exceed 16 points throughout the entire game, but Malthouse said his side didn't have enough players "in touch or in form or consistent enough" when it pushed forward.
"We didn't deserve to win today," he said after the game.
"Well done to Geelong, they are a very good football side for a start, but I half suspect that is close to our worst game for the year.
"We had some players who were respectable, who were in the category where you could say they were okay.
"We had too many players in the category today that were ineffective, and not only ineffective, but [their] decision making, tackling and ball-carrying was probably at the lowest [standard] we've had."
Malthouse said Anthony Rocca was "thrashed" by the in-form Matthew Scarlett, but he also took aim at the Magpies' small forwards, calling their crumbing "second-rate".
He refused to blame the loss on a poor showing at training on Friday or the number of youngsters in the side.
"Our strategies and our game plan today were in place, but we failed to measure up," he said.
"We were terrible. We gave the ball back to them. We kept on giving the ball back to a side that you just don't want to give the ball back to.
"Our [decision-making] today was quite poor, and we just didn't give ourselves a chance to win the game."
Malthouse said the players "didn't support their team" throughout the match, which Geelong led at every change, and was critical of the fact his side could get within 16 points but not finish the task.
"I would have liked to be better to test them. We couldn't test them today. We didn't test them at all," he said.
"When they had the football, they hurt us. When we had it, we didn't. When there was a loose football, they were clean, we weren't, and our tackling today was as poor as it's been for the year.
"Is that because they're quick and strong-bodied? Perhaps. But you've still got to be better at that. We were very poor in those areas."