The Briton, winner of the two previous races in Monaco and Montreal, will start in 10th place after clipping a wall and breaking his car's suspension while Mercedes team mate and rival Nico Rosberg took pole position.
Hamilton also ran off the track twice.
The champion is nine points adrift of the German after seven races and hoped he might be able to regain the lead in Baku but that looks a tall order now unless misfortune strikes Rosberg.
"It just wasn't a good one," Hamilton told reporters.
"It was nothing to do with anyone else, it was just me not doing good laps," he added.
"I just couldn't get into a rhythm today. It wasn't just in qualifying, it was in practice as well. Just an off day, unfortunately. An expensive day, but an off day today."
Hamilton had been quickest in Friday practice and on Saturday morning, but said some overnight changes had affected the car's handling and meant he could not brake at the same places as previously.
"It was just one of those bad days," agreed Mercedes team boss Toto Wolff. "He was blindingly fast in the first sector but couldn't put the sectors together."
Sunday's race in Baku should see plenty of action, with the circuit's 2km straight the longest in the sport, but there is also the risk of frequent interruptions.
"The race I’m sure is going to be very exciting," Rosberg told reporters.
"It’s one of the easiest tracks to overtake, so there’s going to be a lot of changing places I think, probably a lot of safety cars as well, exciting re-starts and everything."
The German side-stepped attempts to get him to comment on Hamilton's remarks on Friday that some drivers -- Rosberg included -- were 'moaning' too much about track conditions and safety.
The Briton had also explained how he saw no point in inspecting the track on foot and questioned the value of simulators.
"Fine. It's his opinion," said Rosberg, who said he was unaware of the comments until after qualifying. "I was definitely one of the guys questioning today and I still do.
"Everybody has their own approach. He's a three times world champion so he must be doing something right."
(Reporting by Alan Baldwin, Editing by Ken Ferris)
Share
