"I think [the decision came] more from the heart probably", he said.
Red Bull's Max Verstappen claimed fifth, but he was involved in the race's most controversial moment, as he crashed into team-mate Daniel Ricciardo at the second corner, forcing the Australian to retire.
Mercedes' strategy differed markedly from that of Ferrari, who used Kimi Raikkonen in second place as a buffer to protect Vettel even though the Finn was faster.
Vettel won in Hungary two years ago and will hope that the trend continues that no driver wins two races in a row this season.
However, Hamilton, who finished fourth, admitted it was "a grey area" given the gap he established to Bottas after passing him.
Speaking on the podium after the race, Bottas was anxious that the increasing gap between the pair would mean a change in positions would be impossible due to traffic and a closing Max Verstappen.More news: More White House drama as Trump replaces Reince Priebus
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The Mercedes duo has won six out of the ten races (Hamilton: 4, Bottas: 2) thus far as the German team leads the FIA Constructors' Championship with a tally of 330 points over Ferrari (275) and Red Bull (174).
Memories of Monaco in May, where Ferrari romped to a one-two finish while Hamilton could manage only seventh, remained raw, but Mercedes team boss Toto Wolff said the situation was not that dramatic.
After Hamilton's comfortable homecoming victory at Silverstone, the Briton was expected to take charge of the world title race.
In the morning session, Ricciardo was 0.234 seconds quicker than Raikkonen and 0.372 ahead of Hamilton on a Hungaroring circuit that proved slippery despite warm weather conditions.
"Slowing down seven seconds was tough and I was nervous of losing a place to Verstappen but fortunately I didn't". "I like this track a lot and it's been really enjoyable", Vettel told DPA. But his final stint was made much easier by the Ferrari behind him.
Ultimately, Hamilton let Bottas back past in the final corner and, on paper, gave up three potential points in his championship fight with race victor Sebastian Vettel.