The Mercedes driver, who clinched his latest title in Texas two weeks ago and had nothing at stake in the race at Interlagos, was handed a five second penalty for the penultimate lap incident.
“I fully accept the responsibility. I fully accept I was coming from behind so I’m the one that touched him, not the other way round,” said the 34-year-old Briton.
“I massively apologise to Albon. I went for a move... the gap was kind of there, but obviously it closed right at the end and completely my fault.
“It’s probably the first time I’ve come together with someone for a long, long time... I went straight to him after the race to apologise.”
Hamilton was demoted to seventh, his 32nd consecutive finish in the points and one short of his own record, while Albon ended up 14th.
“His time will come,” said Red Bull team boss Christian Horner.
Albon said Hamilton, on fresher tyres, would probably have got past anyway further down the road but third would have been his.
“It wasn’t meant to be, next race,” he said.
The race was won by Red Bull’s Max Verstappen, the 22-year-old Dutch driver’s third victory of the season and first from pole, with French 23-year-old Pierre Gasly the runner-up for Toro Rosso.
Albon, also 23, had been second when the collision occurred.
“I think it was a great race and it’s great again to see the youngsters coming and driving so well,” said Hamilton. “I’m battling as hard as I can to stay in the mix.”
Hamilton has still won 10 of the season’s 20 races so far but he recognised that Red Bull and their Honda engine partners were too quick.
“Max did a fantastic job today. They (Red Bull) just outclassed us in terms of overall performance. We couldn’t keep up with them on the straights,” said the Briton.
“Honestly, I raced my heart out. I gave it everything. I left nothing on the table and I took a lot of risks today, as you saw.
“We threw everything and the sink at it. Honestly, we could keep up with them in the corners but they were outshining us on the straights, therefore I don’t think there was anything we could do.”
