Hamilton scraped through to the second stage of qualifying for the Emilia Romagna Grand Prix by just four-thousandths of a second, but could not make it through to top-10 shootout.
A red flag after the initial runs in Q2 gave time for incoming rain to scupper any chance of improving lap times, leaving Hamilton 13th, two places behind Mercedes teammate George Russell.
It marked the second time in four races Hamilton failed to reach Q3, having been knocked out in Q1 in Saudi Arabia, and was the first time since Japan 2012 that Mercedes didn't get a car into the final stage of qualifying.
"It wasn't a great session, naturally it's disappointing," Hamilton said.
"[You] come here with optimism and you know everyone is working really hard at the factory, and things just don't come together.
"It's disappointing. I think we underperformed as a team today. There are things that we should have done that we didn't do.
"Anyways. We'll work as hard as we can to move up in the sprint race. It's going to be a difficult race, but hopefully tomorrow is better weather-wise, and who knows, maybe we'll move our way forwards."
Hamilton and Russell will have the chance to move forward during the 21-lap sprint race tomorrow, the results of which will then set the grid for Sunday's grand prix.
Asked if the sprint meant there was still a chance to rescue something from the weekend, Hamilton replied: "We'll just keep working hard. Each weekend is a rescue."
Hamilton was seen speaking with Mercedes F1 chief Toto Wolff at the back of the garage after dropping out in Q2, but was reluctant to share the contents of their conversation.
"It's all internal stuff," Hamilton said. "So I'd rather not share that."
Russell explained that he struggled chiefly with tyre temperature through qualifying at Imola, with the recurring red flags not helping Mercedes to build up much of a rhythm.
"It was a bit of a shame with how the red flags panned out today," Russell said.
"But if there is a weekend to not be where we want to be, a sprint weekend is the one to do it. [It's] not ideal, but we got a chance to recover these positions tomorrow."
Russell was also uncertain the sprint race would offer much of a chance for Mercedes to move forward, noting the lack of overtaking chances there often are in the Saturday events.
"It's going to be a bit tricky going into the race tomorrow," Russell said.
"Usually in these sprint races, not so much happens. It'll be interesting with these new cars if we can follow a bit closer.
"But I don't think there's enough laps with enough degradation for us to take our advantage where we're generally stronger compared to our current rivals, which this weekend aren't the top two teams.
"So let's see what we can do. We've got Sunday as well. [We] can only go up."
