Klopp decided to miss the fourth-round replay because it fell during the Premier League’s winter break.
A Reds side with an average age of 19 years and 102 days set up a tie at Chelsea with a 1-0 win.
“There was a message at half-time and at full-time [from Klopp],” said under-23s boss Neil Critchley.
“There was a message before the game that Chelsea away could be an opportunity for one or two of them and they put in a performance tonight.”
There was at least one of Klopp’s senior players in the sell-out 52,399 crowd, with James Milner offering his support sat behind the home dugout.
“He trained with us yesterday and he asked whether he could come along,” added Critchley, who oversaw the game for Liverpool.
“He was giving words of advice, he was getting right behind the players. He was vocal in the dressing room. He was animated. He was vocal behind me, I could hear him.”
Ro-Shaun Williams’ own goal was enough to send a Liverpool side containing seven teenage outfield players through against their League One opponents.
Liverpool right-back Neco Williams, whose long ball forward led to the goal, said it was a night that his team-mates would remember for “a long time”.
The result means the Reds are still in the chase for three additional trophies, having already won the Club World Cup and Super Cup.
They have a 22-point lead at the top of the Premier League and are in the last 16 of both the Champions League and FA Cup.
“The lads were excellent and hopefully we will do the same against Chelsea in the next round,” said 18-year-old Williams.
“Our aim is to win the FA Cup. I think the [senior] lads will have been extremely proud of us and hopefully us young players will get a chance again.”
Aged 19 years and five days, Toxteth-born Curtis Jones became the youngest first-team captain in Liverpool’s history.
“All the boys went out there and showed belief, character, showed everything that the manager looks for in his players,” said Jones.
“I was grateful to become the youngest captain of the team but most importantly we came away with the win with a great performance.
“The boys showed heart, character and a hard decision for the next game.”