The seven-time world champion could only set the eighth-fastest time in qualifying as he remained well off the pace of Mercedes teammate George Russell, who was an encouraging fourth.
Hamilton was slower than Russell in two of the three practice sessions in Jeddah and ended up almost half a second adrift of the younger Briton by the end of Q3.
“I struggled with the car in the high-speed particularly,” Hamilton told Sky.
“But just don’t feel the car beneath me. I don’t feel connected to this car and I can’t get it, so I don’t really know what I’m doing to do about that.”
Hamilton, who will start seventh due to a grid penalty for Ferrari’s Charles Leclerc, added: “It’s miserable. It’s tough.
“I’m giving it absolutely everything – I’m here as late as I can be everyday. I’m preparing the best you can and I just get in the car and I can’t connect with it.
“I don’t really know what to say about it.”
Russell, meanwhile, will line up from third on the grid behind Red Bull’s Sergio Perez and Fernando Alonso’s Aston Martin.
The Mercedes duo were separated by Carlos Sainz’s Ferrari, Lance Stroll’s Aston Martin and Esteban Ocon’s Alpine in qualifying.
“It’s good that George had a good run today and he will hopefully be able to score some good points for the team,” Hamilton said.
“I’ll try and recover tomorrow. It’s a new day, so I’ll give it everything.”
