With his side 2-0 down to a Frank Lampard penalty and an Oscar strike, Allardyce made the changes 10 minutes before the break, Mohamed Diame and Modibo Maiga coming off the bench in place of Joe Cole and Jack Collison.
Maiga wasted the hosts' best chance of the game midway through the second half, stabbing the ball wide from six yards, but overall the changes made little difference as Lampard's second of the game eight minutes before the final whistle extended his former club's winless league run to five matches.
After the game, Allardyce stood by his decision under questioning about the reaction of Cole, who looked particularly frustrated.
"I had to change something, somebody has to come off," he said.
"It's frustrating, every player's frustrated because all every player ever does is think about himself and I have to think about the bigger picture.
"If he's frustrated, that's fine, next time he gets a chance he's going to play so well for me that the last thing I can do is substitute him and that's up to him.
"I brought my captain (Kevin Nolan) off in the end because I didn't think he was as good as he can be, I didn't think he drove the team on as much as he normally does."
Guy Demel's weak backpass to Jussi Jaaskelainen let in Oscar in the build-up to the penalty and the manager was disappointed with the way his side allowed Chelsea to get on top.
"We allowed them to be good after the goal," he said.
"It was our defensive frailty that broke first, by an individual error that as a manager you can't allocate for.
"After that we couldn't get out of our half. We were suffering in front of goal and now we're suffering defensively with errors and we've got to stop that first and foremost.
"At the moment it doesn't matter what we play with in terms of system because we're creating chances and not scoring.
"It got a bit better in the second half we tried to create an opening to rally ourselves and the fans but when the chance came we missed it."
