"My [right front] tyre was dead and I was turning and turning and nothing was happening," Hamilton said.
"I was two or three seconds slower than Nico [Rosberg, his team-mate]. There was nothing I could do. I just had to get to a certain target [lap for a pit stop], which was unfortunate, so I lost a lot of ground there."
Webber's Red Bull catches fire
He added: "If I'd been in the lead I think I'd have been able to stay there, but things just did not go my way.
"We need to figure it out because we are faster than our results."
In the closing laps, Hamilton and Alonso were locked in a battle trying to pass Sauber's Nico Hulkenberg for fourth place.
Hamilton did pass the German with seven laps to go, only to lose the place again immediately on the long main straight.
"There was nothing I could do," Hamilton said. "He was so quick on the straight, he just drove past me."
Korean Grand Prix, day three
Sunday 6 October: Race highlights, 14:00 BST on BBC One.
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