While their set-pieces were below-par, Julian Nagelsmann's men continued to dominate possession but found themselves behind at the break. The visitors had a corner from Vincenzo Grifo which was turned in by Manuel Gulde with a cheeky backheel who celebrated with an 'elbow bump'.
Leipzig brought on Ademola Lookman on for the second half and switched to a 4-4-2 in search of goals. And the former Everton man should have equalised soon after but failed to find the target from six yards out. The hosts seemed to have left their shooting boots at home with Werner, Yussuf Poulsen and Lookman again spurning a total of more than 20 chances.
Just as it seemed it was not going to be their day, Poulsen made up for his earlier miss by heading in the equaliser from Kevin Kampl's cross for his fourth goal of the season.
Despite bringing on goal threats Patrick Schick and Marcus Sabitzer, who netted a brace against Tottenham in their last game in March, Freiburg continued to defend brilliantly.
And there was late drama with the visitors celebrating in the 93rd minute when Robin Koch swept home from close range following a free-kick but it was disallowed for offside against Lucas Holer after a VAR review.
The result means Leipzig remain third but slip three points behind second-placed Borussia Dortmund while Freiburg climb to sixth.
Did the nine-week absence affect the quality of the game? Thankfully it did not for the most part. The hosts may have been wasteful in front of goal at times but their passing and intensity was impressive from the off. Freiburg looked organised and tactically sound defensively and did not look like it was their first game in two months. There were concerns about the stamina issue but both teams held up and the new rule of five substitutes allowed them some respite.
Ademola Lookman looks up in frustration
Image credit: Getty Images
MAN OF THE MATCH
Alexander Schwolow (Freiburg): He commanded his box well, negating any impact from Angelino's crosses. He also made some vital saves including from Werner via his foot and Sabitzer late on. The keeper was helped by the organised back three in front of him.