A Dominik Szoboszlai free-kick, an own goal via goalkeeper Geronimo Rulli and a late strike by substitute Cody Gakpo secured the win.
Slot said afterwards: "You know it is always very difficult to play against Marseille because of the passionate fans they have and the quality of the players. What makes it even harder is they have such a good manager, who always lets his team play so well. We were prepared for that.
"I think in the first half you could see we took the ball three or four times off them in very promising situations, but we couldn't find the player that was completely free. We were in four-versus-three situations a few times and the one time we did find the player, it was fractionally offside.
"The thing that was different for the first time this season than all the other games was that the moment we were having a big chance to score the 2-0 that hit the post, 10 seconds later they had a big chance. Usually this season this ball goes in and we're all complaining, but now the ball went over, and we extended our lead to 2-0 and 3-0. The performance is still the same but the perspective of how people probably talk about us is completely different."
On bringing Mohamed Salah straight back into the starting XI after his return from AFCON, Slot was happy with the Egyptian's performance.
"It helps he is already for so long with us so he knows his teammates and he knows how we want to play. It says a lot about how big of a professional he is that being away from us for a month in a different team, he was so fit to play 90 today. He was close to a goal, a good ball from Cody (Gakpo) and usually that's a goal for him.
"Tonight it wasn't but it didn't harm us because we scored three. I think overall, I saw a lot of very good individual performances, as I saw against Arsenal, as I saw against Burnley and as I saw tonight."