Mohoric, who has won on all three grand tours, pipped Thursday's stage winner Kasper Asgreen of Denmark to the line, breaking into tears after a photo finish gave him the victory a couple of minutes later.
Mohoric's success comes just over a month after his Swiss teammate Mader died following a crash on the Tour de Suisse on June 16. Bahrain Victorious riders Pello Bilbao and Wout Poels also took stage victories in this year's race.
"We started this Tour under a lot of stress after the death of Gino and Matej had the ambition to win a stage," Bahrain Victorious sports director Vladimir Miholjevic told reporters.
"It's stupid to say and could be wrongly interpreted but we lost a team member, a family member and everyone in the team, staff and riders, wanted to honour Gino. He will always be with us. It's something we managed to transform into motivation."
Australian Ben O'Connor was third in a three-man sprint ahead of a group of chasers who were caught by surprise when Asgreen attacked in the second short climb of the day.
FOR GINO
Defending champion Jonas Vingegaard stayed safe in the bunch to retain the overall leader's yellow jersey ahead of Saturday's hilly and treacherous 20th stage between Belfort and the Markstein.
He still holds a 7:35 lead over Slovenian Tadej Pogacar.
A large breakaway took shape on the bumpy roads of the Jura with a group of 30 chasing Victor Campenaerts.
The Belgian was caught, and dropped, by O'Connor, Asgreen and Mohoric who reached the top of the Cote d'Ivory first after jumping away from the peloton at the intermediate sprint.
With 15km left, the trio led a group of nine, featuring Mathieu van der Poel and green jersey holder Jasper Philipsen, by 15 seconds.
They did not look back and O'Connor launched the sprint early, hoping to surprise his rivals, only for Asgreen to get into his slipstream and make his effort 300 metres from the line.
Mohoric followed and propelled his bike to the line just before the Danish rider.
"It means a lot. It's hard and cruel to be a pro cyclist. You sacrifice so much, your family does too, and then you realise everyone is so, so strong. Sometimes you feel you don't belong here," said Mohoric, who paid tribute to Mader.
"We spend more time with our teammates than with our family. (His death) puts everything in perspective and makes you doubt what you do but at the end of the day the world moves on. I really wanted to give my best because he can't anymore."
