The Brit started the final race of the season on pole and led throughout but deliberately slowed his pace in the final laps in a bid to put pressure on team-mate Nico Rosberg.
Hamilton started the race knowing he would need to win, while hoping Rosberg failed to finish on the podium and his lack of pace was designed to open up opportunities for Ferrari and Red Bull to put pressure on his colleague.
The situation prompted his team to order him to speed up as he continued to back up Rosberg towards the onrushing Sebastian Vettel.
In the end it made no difference, with the German taking second to seal the title but speaking afterwards, the three-time world champion admitted he had been left frustrated by the request.
"I don't know why they just didn't let us race. There was never a moment that I felt that I was going to lose the race," Hamilton said. "It is a shame but it was quite clear, their thought process, I don't know what to say.
"I don't think I did anything negative today. I was fighting for the championship, I was in the lead and I was controlling the pace. It was within the rules."