Luyindula produced an improbable diving header to score in the 88th minute after a surging run from Brazilian midfielder Juninho had caused panic in the Bayern defence as they were hanging on to protect a narrow lead in their Group A match.
The result was a fair reflection in the end of both sides efforts in a competitive and keenly-balanced clash in front of a full house at the Stade de Gerland.
Bayern top the very tightly-contested group with five points from their opening three matches, followed by Lyon and Anderlecht on four each and Celtic on three.
Luyindula, 24, a former French Under-21 international who was born in Zaire, came on for striker Sidney Govou after 68 minutes as one of three second half substitutions made by Lyon coach Paul le Guen, levelled Dutch international stirker Roy Makaay's adroitly-taken first half goal for Bayern.
Makaay had struck after 25 minutes to put the German champions in control, but his single goal was not enough for them to withstand a late battering as Lyon threw everything at them in the final minutes.
Makaay's slick strike came at the end of a razor-sharp passing move and sparked a spell of dominant football from the German side who might have added a further goal in the second half when Roque Santa Cruz wasted a clear opening by firing against a post from only 10 metres.
Lyon played a lot of skilful attacking football, but were unable to break down the well-organised and more powerful German side, who survived several scares and goalmouth scrambles, until the final minutes when Luyindula broke through.
CLOSE-RANGE
Then, in the final seconds, Giovane Elber, playing against his former club, forced a superb close-range save from Oliver Kahn when he turned and struck a ferocious shot that the goalkeeper parried away to safety.
Seeking their first win in six Champions League away outings, Bayern had taken early control with a sustained spell of possession play, but found it difficult to create any chances until Makaay put them ahead.
His goal came against the run of play and followed a spell of lively attacking football from Lyon during which Juninho had cut in from the left and and fired a 20-metres shot wide, Giovane Elber had a shot blocked and Juninho, from another solo run, rolled a weak shot wide.
Bayern's power, organisation and artistry on the break were always a danger and they opened the scoring from a decisive first-time passing move that ended with Roque Santa Cruz finding Michael Ballack whose instant pass to Makaay was dispatched past Gregory Coupet before the goalkeeper could react.
The German champions' more physical approach not only earned them spells of valuable possession against the sinuous and skillful, and more individual, approach of the French champions, but also cost them yellow cards.
Martin Demichelis, Santa Cruz and Robert Kovac were all cautioned for heavy and late challenges. They were joined in the referee's book in the second half by Lyon's Florent Malouda and Anthony Reveillere as passions became enflamed all over the pitch.
Makaay's goal lit the game up and chances followed at both ends. Santa Cruz shot wide with a diagonal 18 metres shot, Juninho fired a long-range free kick straight at the busy Oliver Kahn and Mahamadou Diarra hammered a drive at the German goalkeeper as Lyon sought an equaliser before the interval.
In the second half, Lyon raised the tempo even more and introduced striker Eric Carriere whose skill and shooting power added to their threat and helped create the climax in which they finally levelled to take a deserved reward.
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