Seeking to build on their opening 2-1 success over Juventus, Christophe Galtier's side were greeted by a hostile atmosphere in Israel and were nearly on the receiving end of a shock result.
Tjaronn Chery stuck a boot out to open the scoring for the hosts on the 24-minute mark, but PSG would restore parity from half time as Messi pounced on a loose ball to slot home inside the area.
The seven-time Ballon d'Or winner would then turn provider for Kylian Mbappe to put PSG ahead before the final member of the famed attacking triumvirate Neymar wrapped up a 3-1 success in the 88th minute.
Prior to making the net ripple against Maccabi Haifa, Messi had netted against a joint-record 38 teams in the Champions League, sharing the record with long-time rival Ronaldo.
Now, the 35-year-old is the outright record holder in the category after scoring against his 39th team in European competition, and that was not the only record he set at the Sammy Ofer Stadium.
Messi's 37th-minute goal also saw him become the first-ever player to score in 18 consecutive Champions League seasons, and he now boasts 126 goals in the competition in total.
Ronaldo still leads the way at the top of the charts with 140 strikes in Europe's top tournament, but Messi will seek to close the gap while the Portuguese plies his trade in the Europa League this term.
Ronaldo allegedly informed Manchester United of his desire to leave in the summer to join a club competing for Champions League glory, but a concrete offer from such a club did not arrive.
Meanwhile, a stellar start to the 2022-23 campaign for Messi has seen him rack up five goals and eight assists in his opening 10 games for PSG in Ligue 1, the Champions League and the Trophee des Champions.
The ex-Barcelona man now has 16 goals and 23 assists to boast from 44 appearances for the French champions, who are level with Benfica at the top of Champions League Group H on six points.
Prior to PSG's trip to the Estadio da Luz to face Benfica on October 5, Galtier has warned his players that their organisation will need to improve after their slow start against Maccabi Haifa.
"We had a difficult first half. We had a good start with some good situations, but the pitch meant that we made mistakes when coming towards goal and in one-on-ones," Galtier told PSG media.
"We were badly organised, the pressure on the opponent was not good and the team was cut in two. In the second half, we changed things, we exchanged with each other at the break to have a better balance.
"As soon as we were all together, in a much more compact block, things became a bit easier for us. We created situations and it took the quality of our attacking trio to go and get the win."
PSG now prepare to continue the defence of their Ligue 1 title away to Lyon on Sunday evening before the international break.