Mothiba was handed a second successive start in the league for the visitors, as he looked to add to his debut goal.
Strasbourg were looking to build on their win over Amiens on the weekend, and they got the opening goal after 27 minutes thanks to a strike from Kenny Lala.
The hosts were level on 41 minutes when former West Ham United star Dimitri Payet converted a penalty, before Morgan Sanson completed the comeback on the sroke of halftime.
Shortly after the break, Marseille were reduced to 10 men after Jordan Amavi was shown a straight red card.
Strasbourg's equaliser eventually arrived in the 89th minute, with Mothiba picking up the assist for Nuno Da Costa's goal to as the looked set for a point.
However, the hosts secured the win in the first minute of time added on thanks to a strike from Valere Germain.
Paris Saint-Germain 4-1 Reims
Nimes 0-0 Guingamp
Amiens 2-1 Rennes
Caen 2-2 Montpellier