Loic Remy opened the scoring with his 17th-minute effort before Pepe registered his ninth Ligue 1 goal of the season.
The 23-year-old doubled his team's lead, converting Remy’s assist with a left-footed shot in the 28th minute.
The hosts headed into the interval with a two-goal advantage but Traore inspired the Kids' comeback with a goal and an assist after the restart.
The Burkinabe forward halved the deficit for Lyon in the 63rd minute and later assisted Moussa Dembele's late equaliser.
The result left Lille without a win since their 1-0 win over Caen in October while their visitors extended their unbeaten run to six games in the French top-flight.