The German took issue with words that were "not OK" in his eyes from the official, who oversaw the Reds' enthralling 4-3 Premier League victory at Anfield.
After gleaning a 3-0 lead inside the opening 15 minutes, Liverpool were remarkably pegged back to 3-3 as Richarlison headed home from a free kick in added time.
Klopp was infuriated about the awarding of the free kick, and he sprinted to shout in the face of fourth official John Brooks after Diogo Jota restored the hosts' lead.
The 55-year-old was subsequently booked by Tierney, but he alleged that the 42-year-old must have something "against" his team after the game, having been involved in a number of confrontations with Tierney down the years.
Having reviewed audio of the incident, the PGMOL have announced that they "strongly refute" Klopp's allegations, and the German revealed on Tuesday that Tierney told Klopp his celebrations warranted a red card, but he downgraded his punishment to a yellow due to Brooks's presence.
The FA quickly opened an investigation into the matter, and the governing body has now charged Klopp with improper conduct, implying bias and questioning Tierney's integrity.
"Liverpool FC's Jurgen Klopp has been charged following their Premier League fixture against Tottenham Hotspur FC on Sunday 30 April," the FA said in a statement.
"It is alleged that the manager's comments regarding the match official during post-match media interviews constitutes improper conduct in that they imply bias, and/or question the integrity of the referee, and/or are personal/offensive, and/or bring the game into disrepute. Jurgen Klopp has until Friday 5 May to provide a response."
Klopp addressed the comments he made towards Tierney during Tuesday's press conference, admitting that his comments were largely borne out of anger, although he denied that he lied at any stage.
Tierney was at the centre of two controversial on-field decisions on Sunday, as Oliver Skipp was firstly allowed to continue despite catching Luis Diaz with his studs in a dreadful challenge.
With 81 minutes on the clock, Skipp was then the victim of a high boot from Jota, which left the Englishman bloodied, but the Portuguese escaped a red card before scoring his dramatic winner.
Tottenham interim manager Ryan Mason was incensed at the decision not to send Jota off, demanding an explanation from the officials and insisting that Spurs were the better team "by a country mile".
Klopp, who could be facing a lengthy touchline ban for his confrontation with Tierney, has led Liverpool to four consecutive Premier League wins, allowing them to rise up to fifth in the rankings before Wednesday's visit of Fulham.