The 35-year-old, who retires at the end of the campaign after 13 years at Dortmund, came on in the second half and fired home from 25 metres.
Without injured Mats Hummels and Marco Reus, Dortmund took the lead through central defender Neven Subotic in the 19th minute before Kevin Volland's superb volley levelled the match two minutes later.
Serbia international Subotic then gifted Hoffenheim their second goal when he lost possession to Roberto Firmino, who charged through and beautifully chipped keeper Mitch Langerak.
Pierre-Emerick Aubameyang, however, made amends for his team mate's mistake, heading in the equaliser early in the second half before Kehl's superb winner in the 107th minute went in off the post.
Dortmund, last year's beaten finalists, are looking to rescue an otherwise disappointing season by securing a Europa League spot after a dismal Bundesliga campaign.
VfL Wolfsburg dominated but needed a second-half penalty from defender Ricardo Rodriguez to edge past fellow Bundesliga club Freiburg 1-0 and advance.
The Swiss international, who also scored twice in the win over VfB Stuttgart at the weekend, converted a 72nd-minute spot-kick after Daniel Caligiuri was brought down by Julian Schuster.
Holders Bayern Munich, chasing a treble of titles, play Bayer Leverkusen in another all-Bundesliga clash on Wednesday with Borussia Moenchengladbach taking on third-tier Arminia Bielefeld.
(Reporting by Karolos Grohmann; editing by Justin Palmer and Toby Davis)
