With teammate and pole sitter Valtteri Bottas second behind Max Verstappen, the Finn was given team orders over the radio to allow Hamilton, who leads the drivers' standings, to pass halfway through Sunday's race.
The Briton, who extended his championship lead over rival Sebastian Vettel to 50 points by winning at Sochi, called it 'a difficult day' for him and the team.
'Valtteri did a fantastic job all weekend and he was a real gentleman to let me by,' Hamilton told the post-race press conference.
'It's just been such a great weekend for the team. The team have done such exceptional job to have this advantage on Ferrari and have a one-two. Usually, you'd just be elated, but I can understand how difficult it was for Valtteri.
'But really, he did a fantastic job today and deserved to win. But championship-wise, as a team, we're trying to win both championships, and today, it was a real team effort.'
'Did not feel good'
Vettel finished third for Ferrari to lose further ground on Hamilton with just five rounds and 125 points of this year's championship remaining.
It was Hamilton's fifth victory in the last six races and 70th career win as he closes on his fifth F1 crown, but he was full of sympathy for Bottas who was on course for only his fourth career win.
'Naturally, passing him did not feel good in that instant,' Hamilton said. 'I didn't know what was planned for the end ... but honestly, it's very hard to find the right words.
'It's a very strange feeling. We've had a one-two, we've dominated as a team this weekend, the team have done an incredible job and it's never, ever in my whole life how I've wanted to win a race.
'But that's why I just want to shine it onto Valtteri because there's not many teammates who would do something like that.
'The racer inside me wants it to be the other way around. The ruthless killer instinct inside me says: 'This is the way it should be, stop being so soft. This is the way it needs to be.''
Bottas, who remains without a win since topping the podium at last year's season-ending Abu Dhabi Grand Prix, could not mask his obvious disappointment.
'Yeah, difficult day,' a disgruntled Bottas said. 'Obviously a good result for us as a team; we got maximum points. But personally, as everyone saw, it was quite a difficult race.
'We always go through all the scenarios, all the facts. Lewis is now fighting for the championship and we are fighting for the Constructors', so we always have a plan.
'But yeah today is ... it's always difficult to predict what's going to happen in the race, how it is going to go, but it is what it is.'
The man responsible for the controversial team orders was Mercedes boss Toto Wolff who has previously, on multiple occasions, expressed his desire to let his drivers race.
In motorsport, team orders are instructions from the principle which demand drivers to stop racing competitively against each other as they would other teams' drivers.
Wolff again reiterated that desire after the race on Sunday but insisted it was the right decision in the long run.
'You need to weigh it up,' he explained. 'Do I want to be the baddie on Sunday evening for many of the right reasons or the idiot in Abu Dhabi at the end of the season?
'I would rather be the baddie today and not the idiot at the end of the year. Rationally, it was the right decision, but our sporting heart says no.'
How the events unfolded
After a slow pit stop, Hamilton briefly found himself behind Vettel before completing an audacious overtaking move on the German to reclaim his track position.
Shortly after came tense exchanges on the Mercedes team radio, with a clearly disgruntled Bottas ordered to allow Hamilton through and into second place in the race behind Red Bull's Max Verstappen.
Young Dutch star Verstappen had charged through from 19th on the grid after a pre-race penalty but had still to pit, leaving Hamilton effectively in the lead.
Verstappen eventually took a superb fifth place to mark his 21st birthday behind the second Ferrari of Kimi Raikkonen, with his Red Bull teammate Daniel Ricciardo in sixth.
Charles Leclerc, replacing Raikkonen at Ferrari next season, again served notice of his promise with a brilliant seventh for Sauber, with Kevin Magnussen eighth for Haas, ahead of the Force India pair of Esteban Ocon and Sergio Perez.
READ: Valtteri Bottas signs contract extension at Mercedes
It was a subdued Hamilton who was presented with his prize by Russian president Vladimir Putin, with little of the usual celebration next to his unhappy teammate.
But he will move on to the Japanese Grand Prix in Suzuka with a commanding advantage over Vettel, who has seen his chances of a fifth title recede since the summer break in the face of a resurgent Mercedes team and Hamilton's individual brilliance.
Mercedes has also increased its lead in the constructors' championship to 53 points over Ferrari, but that will be little consolation for Bottas, who is still seeking his fourth F1 victory and looked set to achieve it after claiming a brilliant pole Saturday and moving clear of his teammate in the early exchanges.
But with Vettel still a factor and with Hamilton having apparent problems with a blistered tire, Mercedes took its controversial decision.
Team chief Toto Wolff tried his best to console Bottas: 'Valtteri this is Toto - a difficult day for you, a difficult day for us -- let's get together and discuss it later,' he said.
Bottas was able to repel a late challenge from Vettel to remain in second place, with Hamilton rounding off his victory by 2.45 seconds to continue Mercedes domination at the Sochi Autodrom, with five wins out of five F1 races at the circuit.
Putin arrived late and sat next to former F1 supremo Bernie Ecclestone, but on the podium saw close up the fallout of the controversial Mercedes team tactics which decided the eventual outcome and loaded the title odds more firmly in favor of the defending champion.