Leipzig's Timo Werner broke the deadlock when he dribbled past two defenders and fired in a left-footed shot that went in off the post in the 65th minute.
But their joy was short-lived as Freiburg struck twice in four minutes for an unexpected win.
Janik Haberer drilled in from 12 metres in the 72nd minute and before Leipzig could recover, they struck again through Robin Koch, whose maiden Bundesliga goal last week earned a point for his club.
Leipzig now drop to third place on 31, as many as Bayer Leverkusen, who are second with a better goal difference following their 4-1 demolition of Hoffenheim.
In-form Leon Bailey opened their account with a spectacular backheel in the first half before Julian Baumgartlinger added another and Lucas Alario grabbed a double.
Bottom club Cologne continued their recovery with new signing Simon Terodde scoring twice as they eased past hosts Hamburg SV for their third league win in a row.
Terodde also scored the last-gasp winner last week and Cologne climbed to 12 points, four points away from the relegation playoff spot.
Bayern, top on 44, can increase their lead with a win over Werder Bremen on Sunday while Borussia Dortmund are fifth after their 1-1 draw at Hertha Berlin on Friday.
(Reporting by Karolos Grohmann; Editing by Christian Radnedge)
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