The Spaniard struck from close range in the dying seconds of the game, rewarding Marseille for their constant domination.
An over-defensive St Etienne side had taken the lead in the 16th minute thanks to a splendid Pascal Feindouno goal.
The Guinea international took advantage of Fabien Barthez's tendency to play far from his line to beat the French international goalkeeper with a cunning lob.
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In the fifth minute of time added-on, 21-year-old Koke finally relieved the 57,000 Marseille fans when he scored from a cross by Senegal's Sylvain N'Diaye.
Marseille remain in fifth place in the standings, five points behind leaders Olympique Lyon who beat Caen 4-0 at home on Friday, while St Etienne remain 17th.
Lille, who beat Bastia 2-1 on Saturday, are second behind Lyon only on goal difference.