Gomez made only his second Premier League start in a year by helping the Reds earn a third successive clean sheet in the 2-0 win over Watford at Anfield on Saturday.
The 22-year-old had become a regular alongside Van Dijk at centre-back before suffering a fractured leg at Burnley last December.
Klopp has revealed he held talks with the player over his part in Liverpool's long-term plans.
“Oh, we spoke, we spoke a lot," said the Reds boss, who is now in Qatar with his squad to prepare for this week's FIFA Club World Cup.
“In a very good team, which we obviously are, the train doesn't wait. That means other players showed up, and I don't think anybody thought really we should put Joel (Matip) on the bench. It is just that the boys are incredibly talented.
“The boy is still young, that is not the reason - it's just that you keep rhythm and you keep players together. But these two, Joe and Virg, they like each other a lot, and they can play sensationally well together.
“And Watford was an especially difficult game - Deeney! - and how you can imagine they play one ball direction. And the balls that came into Virgil were only because of the wind, all the others came to Joe, and Deeney goes up.
“This outstanding skilled boy has this kind of improvement in these moments, but he hasn't played consistently for a while.
"But he has improved a lot there, and that's all good. Football-wise he's an exceptional player, but against Watford you could see he had to fight, and fight to keep concentrated."
Klopp added: "Last year, at the start of the season the partnership was Joe and Virgil right, and they did exceptionally well.
“Put him on the right side, we thought it made sense because we play (regularly) at least three centre-halves, and it was important for him to have rhythm for the time now - that period over December and January.
"And in one of these games he played at right-back at Burnley and got that bad injury which took him out for a while."