Balotelli rose to powerfully head in a corner five minutes into injury time, shortly after Lille striker Nicolas Pepe had netted his second goal of the game through the legs of keeper Steve Mandanda following a quick counter-attack.
Balotelli, who started on the bench after joining from Nice until the end of the season, remonstrated with referee Amaury Delerue moments after the final whistle for not allowing more time to be played.
Delerue had his hands full all night, having taken the players off 10 minutes into the second half after a firecracker was thrown from the crowd and landed near a linesman and two Marseille players .
Pepe scored his first goal from the penalty spot in first-half injury time. His double took his tally to 15 in the league, two behind top scorer Kylian Mbappe of Paris Saint-Germain.
Marseille's impressive winger Nemanja Radonjic had an early goal disallowed following a video review.
The defeat leaves Marseille, which had Florian Thauvin sent off after 67 minutes, in seventh place but it could slide further after the weekend matches.
On Sunday, runaway leader PSG hosts Rennes. Victory will restore its 13-point lead over Lille, having played two games fewer.