After the break, the Wolverhampton Wanderers striker, who had dominated his matches until the final, scoring 13 goals, continued to press for an equaliser.
It finally came from Adama Traore thanks to a brilliant backheel assist from Jota's in-game character.
With both sides level after 90 minutes, the tie went to a second match to be decided by a Golden Goal.
After Jota had missed a couple of excellent chances he won it thanks to a 67th-minute strike from Raul Jimenez.
The winner's prize fund for the Invitational will be donated to the #PlayersTogether initiative, created by Premier League players as a collective way of generating funds for the National Health Service and distributing them where they are needed most.
SF1 Trent Alexander-Arnold (LIV) 3-2 Raheem Sterling (MCI)* | Report and highlights
SF2 Diogo Jota (WOL) 4-1 Dwight McNeil (BUR) | Report and highlights
Final Trent Alexander-Arnold (LIV) 1-2 Diogo Jota (WOL)*
Fans can relive the action from all the ePL Invitational matches on the Premier League's YouTube channel.
We would also ask anyone inspired to play FIFA 20 to take regular breaks from gaming, every 45 minutes.