The Gelsenkirchen outfit have taken just one point from their opening three games in the Bundesliga, but a 3-2 win on Tuesday night saw them advance to the group stages of Europe's elite competition 4-3 on aggregate.
Keller now wants to take the confidence gained from that first competitive win of the season into their domestic form.
"First and foremost we're very, very happy to have achieved the objective we have worked and fought so incredibly hard for over the last six months," he told a post-match press conference.
"It's a vital lift for the team and I think we can take some positives from it for the next few matches."
Adam Szalai's first-half opener set the Germans on their way, and despite a 53rd-minute leveller from Stefanos Athanasiadis and the dismissal of Jermaine Jones, they regained control through Julian Draxler's 67th-minute strike.
A 79th-minute effort from Kostas Katsouranis gave Salonika hope but Szalai's second in the final minute sealed victory for the visitors.
"It wasn't an intoxicating performance, that's for sure," Keller said. "There was a huge amount at stake and that had a noticeable effect on the players.
"Nevertheless, we had the proceedings well under control in the first half and got the goal. If anything we ought to have taken the lead in the first two or three minutes.
"We then came out for the second half and conceded the equaliser due to a positional error.
"The red card against us came at a very bad time, of course. We had already gone 75 minutes with 10 men at Hannover due to a sending-off."
PAOK boss Huub Stevens, who was replaced by Keller at the Veltins-Arena in December 2012 was proud of his team's performance despite seeing them drop into the Europa League.
"Obviously we're disappointed not to have gone through but I have to pay my players a huge compliment," he said.
"They played very well. Schalke didn't make it easy for us. It speaks highly for us that we were able to live with a team of Schalke's calibre.
"We would have loved to have qualified for the Champions League but I'm pleased that we can now play in the Europa League.
"We showed that we're on the right track and we will continue to build on that. A performance like that will give the players confidence as they get used to playing two matches a week."