Brondby has now picked up five out of nine possible points since Frederik Birk took over the helm during the winter break after the dismissal of Jesper Sorensen.
Without the late equaliser Brondby would have been pushed back to seventh spot in the Superliga, but one point was enough to secure fourth spot before the last two rounds of the regular season.
The home side was almost caught napping already after four minutes when Jesper Cornelius came face to face with Brondby keeper Patrick Pentz but Cornelius failed to keep his cool and squared the ball past the post.
Brondby controlled the game throughout the opening stages with young Noah Nartey as the big orhestrator in midfield, but the home side failed to turn their dominance into goals on the scoreboard against a well-organized Lyngby side who were basically content just to defend their one point in the bag.
But then after 56 minutes Lyngby brought the passionate Brondby crowd to silence when Frederik Gytkjaer who had replaced Michael Opoku at the start of the second half was put clean through and Gytkjaer cooly placed the ball beyond the reach of Pentz in the net.
Brondby upped the pressure for the remainder of the match but never really looked dangererous until deep into injury time when a loose ball ended at the feet of Vanlerberghe who first-timed the ball into the roof of the net.
Brondby is now under pressure for their last two matches of the regular season against Randers and Silkeborg to secure a Top 6 finish which would give them a ticket for the Championships Playoffs.