The Bees booked a dream west London derby with Rafael Benitez's side thanks to Clayton Donaldson's 76th-minute winner.
Paul Hayes had given the hosts the lead just before the half hour, only for Barry Corr to head home Ryan Leonard's cross to level after the interval.
Kernaghan said: "We will start to think about Chelsea in the week before that game but if we stick to the plan that we come up with we will be in with a decent chance.
"In the meantime, it's a really good thing that we have the league leaders in Tranmere and then Leyton Orient coming here and going into those games that performance was excellent.
"On another day we would have had five or six but their keeper was in great form and they have made it very difficult for us over two games.
"We always felt we needed a second goal and that was the only frustrating part. But we didn't panic, bided our time and got our reward in the end."
The Bees' progression means their trip to Stevenage, due to take place on Saturday January 26, will now be rearranged.
- Sports & Recreation
- Ryan Leonard
- Clayton Donaldson
- Paul Hayes
- Barry Corr