Sadio Mane and Mohamed Salah both scored in the space of three minutes in the second half to send the Anfield club back to the top of the Premier League.
England midfielder Henderson forced the breakthrough as he teed up winger Mane's headed opener shortly half-time with a delicate cross to the far post.
The 28-year-old has thrived in a box-to-box role in recent matches and his assist further justified Klopp's decision to move him further upfield.
"I've said it since the first day I arrived and my opinion hasn't changed: he's a fantastic skipper for this team," Klopp told Sky Sports. "On and off the pitch, he's fantastic.
"He's played so many positions - which I forced him to do - and he was still very, very important. There was not one part of him that was not important.
"In the last three games he's obviously on fire, which is good."
Liverpool's win was their sixth straight in all competitions and first at home to Chelsea in the Premier League since 2012.
Henderson told Sky Sports: "It's obviously another big win for us in another big game.
"We have to concentrate on ourselves, work hard in training and do the business when we play at the weekend or in midweek.
"We're enjoying it, that's the main thing. We've got to keep doing it."
They currently hold a 2-0 aggregate lead over the Portuguese side and will be looking to advance to the last four of the competition for the second year running.
Following the clash against Porto, attention then returns to the Premier League ahead of their fixture against Cardiff City on April 21.
They then end their Premier League with games against Huddersfield, Newcastle and Wolves.