Jota was chosen over Darwin Nunez to lead the line against Enzo Maresca's men, but he appeared to take a whack to his side early doors when he was brought down by Blues defender Tosin Adarabioyo.
The challenge occurred when Jota was about to run through on goal, a similar incident to the one that Arsenal's William Saliba was sent off for against Bournemouth, and Liverpool fans inevitably screamed for Tosin to be given a red card.
However, referee John Brooks deemed the challenge only worthy of a booking, as Tosin was being sufficiently covered by a couple of blue shirts around him, although Jota came off much worse for wear.
The 27-year-old initially tried to play through the pain, but he was forced to call it quits on the half-hour mark, as Darwin Nunez came into the XI for the remainder of the contest.
Slot expects Jota to miss RB Leipzig clash
Speaking to the media in his post-game press conference, Slot admitted that he was still in the dark about the severity of Jota's problem, but he expects the attacker to miss Wednesday's Champions League clash with RB Leipzig.
"Diogo had to be substituted and I am not sure what it is, but I'd be surprised if he is there on Wednesday," said Slot, who also revealed that his side were dealing with a handful of fresh worries before kickoff.
The Merseyside giants were already missing Alisson Becker (hamstring), Harvey Elliott (foot) and Federico Chiesa (unspecified) for the visit of Chelsea, while Alexis Mac Allister was also reported to have missed training in the lead-up to the game.
The Argentine was fit enough to come off the bench, but true enough, Slot confirmed that he had been feeling under the weather, while Trent Alexander-Arnold was carrying a knock and Conor Bradley missed out entirely for unexplained reasons.
"I have a lot of confidence in this team, but you also saw today - after the international break - that we have some problems," the Liverpool manager added.
Liverpool nearly in right-back crisis before Chelsea win
"Conor Bradley is not in; Trent [Alexander-Arnold], you probably don't know, was also not training in the first days after he came back, so he was a bit of a doubt before we started the game. [And] then we had Macca [Alexis Mac Allister] being sick."
Alexander-Arnold lasted until the 81-minute mark before replacing Joe Gomez, who may now come into contention for a start in midweek if his teammate is not deemed ready for two starts in four days.
In spite of their new fitness concerns, Liverpool made it 10 wins from 11 under Slot thanks to a Mohamed Salah penalty and Curtis Jones finish either side of a Nicolas Jackson leveller, leapfrogging Manchester City back to the top of the Premier League table in the process.
The Reds maintain a one-point lead over the reigning champions and have also opened up a four-point gap over third-placed Arsenal, whom they meet at the Emirates in next Sunday's Premier League blockbuster.