An Edinson Cavani brace and Thiago Motta's goal made it four wins from as many matches for PSG at Parc des Princes on Friday.
Cavani put PSG ahead from the penalty spot in the 20th minute but the hosts struggled in the first half, before the Uruguay international and Motta sealed the three points following the interval.
"We are happy," head coach Emery told beIN Sports. "Our objective was to finish [ahead of the international break] top of the table.
"Up against a team that had won their first three matches, we won without conceding a goal.
"However, we did not master things as well as we wanted to in the first half. We lost out often in the transitions.
"Our positioning was better in the second half. The team was better overall. We were in control and certain details made the difference. There are a lot of things to analyse and to improve. It is good."
World-record signing Neymar was not among the scorers for PSG having netted three goals in two games but Emery said: "The first two games he felt very good. Against St-Etienne, it was another process, which allows him to learn."
Neymar could be partnered alongside Kylian Mbappe in the coming weeks as the 18-year-old Monaco sensation continues to be linked with a big-money move to PSG.
Asked about Mbappe, who scored 26 goals in all competitions as Monaco won Ligue 1 last season, Emery replied: "I'm happy with the players we have. If something changes, it is to improve us. If we finish the window with the players here with us, I'm happy."
Cavani added: "It's good to start the season this way. These victories give us even more confidence. With Neymar, we are bigger. We must continue to improve."