The result lifted Bayer, who were hammered 4-1 by Wolfsburg at home on Tuesday, two places up to third on 56 points from 29 games, eight behind champions and leaders Bayern Munich, who play Fortuna Duesseldorf on Saturday.
Freiburg stayed eighth on 38 points after stretching their winless run to four games since the Bundesliga restarted on May 16 following a two-month lay-off caused by the COVID-19 pandemic.
A dull first half produced a solitary chance for Freiburg in the 43rd minute, when Lucas Hoeler fired wide of the far post with only Leverkusen keeper Lukas Hradecky to beat.
With Bayer gaining the upper hand after taking the lead, Julian Baumgartlinger had a goal disallowed for the visitors in the 63d minute for a push on Dominique Heintz and that finally seemed to spring the home side into action.
Nils Petersen missed Freiburg's best chance to equalise in the 87th minute as keeper Lukas Hradecky parried his scuffed shot from 10 metres and the home side's Lucas Hoeler was also guilty of poor finishing in the 43rd, firing wide with the goal at his mercy.
In Saturday's other standout fixture, former champions Werder Bremen, who are in danger of relegation as they are six points adrift of the safety zone, visit ninth-placed Schalke 044 who are on a 10-match winless league run.