The pair were running close together on track in fifth and sixth in the closing stages of the Suzuka race as the fast-charging Sainz closed up behind them.
Hamilton, who was on better tyres, was eventually allowed past Russell, but was then immediately ordered to slow down to try to keep Russell within DRS range so he would not be such a sitting duck against Sainz on the straights.
This came just one week after Sainz himself brilliantly used to tactic to give Lando Norris a boost, which successfully staved off an attack from Mercedes.
But Hamilton questioned the tactic as he felt that not being allowed to pull clear and build up a big enough gap against Sainz was completely the wrong thing to do.
"I don't think that was a good idea at all," explained Hamilton. "When they suggested it to me, I knew that they had obviously thought of it from the last race, and it made no sense.
"I needed to get as far clear ahead as possible and I was on my way. I was around two seconds ahead and they asked me then to give George DRS, so I had to come off the gas down the straight to get him 0.8s behind.
"He got DRS, but got overtaken, which was going to happen because he was on a one-stop and we were on a two.
"Then he [Sainz] got past him and he was right on my tail, so yeah, not ideal. It made it very hard for the last couple of laps, but I think as a team we've got to be grateful for a fifth and seventh. It's better than a sixth and seventh."
Hamilton felt that the whole situation regarding him and Russell could have been handled better by Mercedes because they both lost time racing each other at that critical phase of the race.
"We should have swapped around earlier and I should have got as far ahead as possible to keep the gap as big as I could to the Ferrari," he said.
"I think if we had inverted, maybe George would have had a better time holding him behind maybe, but because he was trying to fight me and damaging his tyres then I think it just made it all complicated.
"The fact is we're not fighting each other in the teams' championship, as the drivers' is not important where we are.
"What's important is one of us finishes ahead of the Ferrari to keep the position [in the constructors']. So today we really needed to work as a team."
The close battle at the end of the race came after some frenetic battling between the pair earlier in the grand prix which included one moment where Hamilton appeared to push Russell wide through Spoon Curve.
Hamilton admitted he had been tough with his team-mate, but did not think he had over-stepped the mark, as he also said his performance had been compromised a little in a collision with Sergio Perez on the run down to the first corner.
"I was definitely aggressive, but I think it was good racing," he said. "Honestly I shouldn't really have been in that position.
"But I think I've picked up a little something on the right front and it just kept snipping the front right at the last corner and Turn 9. Then it wouldn't turn through the hairpin.
"All weekend I've been good through there, but I was turning and nothing was happening. Definitely struggled on track with the balance. But it was a good battle, a little bit aggressive, but it was what was needed to get position."
