"I don't think there was an awful lot missing, but we weren't quick enough," he explained.
"It was difficult in the wet and difficult to squeeze everything out of the car.
"I think the laps that I had were fine, but just not quick enough. In the wet conditions, we are not as confident as in the dry, so there's work to do.
"It was a tricky session and it could have been anything. I think in the dry, we were pretty much in control. Obviously, it wasn't dry this afternoon, so it wasn’t meant to be.
"But we will see tomorrow. It's not easy. It's better if you start from first, but we're starting from fourth so we're focussed on winning from fourth."
Vettel was out-qualified by Ferrari team-mate Kimi Raikkonen for only the third time this year, but the Finn was also not happy.
"There was definitely a chance I could have put it on pole in these conditions," said Raikkonen, who has had eight podium finishes at the Hungaroring.
"I was unlucky with the last run. We changed tyres and there was a lot of grip, but we got stuck behind the Haas -– there was a lot of spray and it was impossible to see or improve."
Hamilton leads Vettel by 17 points in the drivers championship.