N'jie registered his third goal of the season in the French elite campaign for Rudi Garcia’s men when he found the net two minutes before the quarter half-hour mark.
The 24-year-old fired a shot that caught goalkeeper Alexandre Letellier napping after connecting well with Morgan Sanson’s pass.
The former Olympique Lyon star was replaced by Valere Germain in the 37th minutes after picking up an injury in the challenge.
Ekambi restored parity to his side when he found his way past the defenders to smash home his shot in the 71st minutes.
The tense game saw Argentine Lucas Ocampos getting the march order while five other players were cautioned.
With the results, Marseille are placed fourth on the log with seven points from three games while Angers occupy the seventh position having garnered five points from the same number of matches.