The three-time world champion finished 6.6 seconds behind victor Sebastian Vettel at the Sakhir Circuit, thanks largely to a five-second time penalty for driving "unnecessarily slowly and erratically" in the pit lane as he tried to prevent Daniel Ricciardo from getting past. He was not happy with his McLaren car's performance, though, saying "I've never raced with less power in my life" over the radio. Bottas came in first, which pushed back Hamilton's stop.
"Ferrari did a great job".
"The pit lane was my fault, so apologies to the team for losing the time there".
Team boss Toto Wolff confirmed to Sky F1 that a problem on the grid had caused the Finn's rear tyre pressures to be too high, leaving his W08 hampered by oversteer.
It was the second win in three races for Vettel, but it could be argued the result would have been different if Hamilton hadn't got a five second penalty for holding up Daniel Ricciardo on the pit entry. Max Verstappen, who was strong in the previous race, did not finish after an issue with his brakes in lap 11. It was a good start - our pace was key today to win.
The victory was the four-time world champion's second of the season and 44th of his career.
"Sebastian was in my blind spot so I didn't know where he was", Hamilton said.
Ferrari chose to bring Vettel into the pits for an early stop on lap 10.
On the next lap Lance Stroll in his Williams and the Toro Rosso of Carlos Sainz came together to bring out the safety auto and start a mad dash for the pits.
The 32-year-old Briton said he had felt good on the podium, where he was joined by Mercedes team mate Valtteri Bottas, but the mood had changed as the evening wore on and he relived what went wrong.
"That is the interesting question that we need to analyse at the moment and I don't want to pre-empt what the consequences will be, or if there will be consequences".
"I know that gap that was there doesn't just come from driving". Hamilton, who won in China last weekend, crossed the finish line 6.6 seconds behind.
Mercedes have rules of engagement for its drivers but previously have always allowed them to race without orders.
The German star now leads the title race with 68 points ahead of Hamilton on 61.
Hamilton chased Vettel all the way to the end but was ultimately hampered by a mistake earlier in the race.
"Our generator broke on the grid and we couldn't bleed Valtteri's tyres so we were starting with the completely wrong tyre pressures on his auto", said Mercedes chief Toto Wolff.