Bayer had 60 per cent possession on Saturday, 11 corners and took 13 shots, including five on target, but Fahrmann marshalled Schalke's defence expertly, ensuring the visitors won and moved within three points of Leverkusen in the Bundesliga standings.
Keller conceded after the game that his team failed to match Leverkusen early and gave all credit to Fahrmann for ensuring the hosts did not take the lead.
"We didn't start the game well," Keller told Schalke's website.
"Leverkusen were the better team in the opening stages but we had a bit of luck on our side and a fantastic goalkeeper too, which is why we didn't fall behind.
"After we scored the opening goal we did really well for the rest of the first half and hardly gave anything away.
"We knew Leverkusen were going to put us under a lot of pressure at the start of the second half. I take my hat off to my team for the way they dealt with it."
After Schalke weathered the early storm from Leverkusen, Leon Goretzka put the visitors in front in the 28th minute.
An own goal from Schalke defender Felipe Santana saw Leverkusen draw level in the 66th minute but Klaas-Jan Huntelaar struck just eight minutes later to ensure Keller's team triumphed.
Leverkusen head coach Sami Hyypia was left frustrated by his team's inability to take their chances, which saw them lose for the third time in five Bundesliga matches.
"We were the better team until we conceded the first goal and had the best chances to score," the Finn said.
"But we were too nervous and our movement wasn't that good.
"After the break we were the better team again but that's not how football works. We didn't take our chances, whereas Schalke did."
