Leaney enjoyed yet another bogey-free round, his third of the tournament, and added five birdies to finish at 22-under-par. His only blemish in 72 holes of the event was a bogey on the 18th on Saturday.
'I really was quite nervous starting off the day,' said Leaney, who visited the winner's circle for the first time since the 2000 Dutch Open.
'I wasn't sure how I was going to play and got a really bad lie in the bunker on the first right under the lip. But I managed to get that up and down and that set the tone for the day. Made a very good putt there and birdie on the next and kept things going from there.'
Cejka, trying to become the second German to win the host country's tournament, needed birdie on the last to catch and force a playoff with Leaney.
He pulled his approach well left and into a bunker and could only manage par, though good enough for sole possession of second place.
'I am more than happy because I achieved my goal of playing all four rounds under 70,' said Cejka. 'I knew I needed to hit my wedge close on the last, but pulled my shot a little. I was a little nervous, but knew I could get up and down and holed a good putt on the last to finish second.'
Third-round leader, former NCAA All-American Paul Casey, bogeyed three holes in the middle of his round to fall out of contention. His final-round 71 put him at 20-under-par and in a tie for third, two strokes behind Leaney.
Also two back of the winner were 44-year-old Ian Woosnam of Wales and 20-year-old Englishman Nick Dougherty.
Woosnam, who held the second-round lead, shot his second 68 of the weekend but a couple of costly bogeys, on the 14th and 16th, cost him a shot at the title.
Dougherty, dubbed 'little Nick' due to his close association with Nick Faldo, had one of the day's best rounds with a 6-under-par 66. It was the second best finish of his very young career and vaults him 10 spots on the European Order of Merit, from 41st to 31st.
Colin Montgomerie, who said his back was in serious pain Sunday and admitted his Ryder Cup play might be in jeopardy, carded his third successive sub-70 round and was alone in ninth place.
'My gut feeling is I'm going, but I'll make a decision next week,' said Montgomerie. 'If I can't play five times for Sam (Torrance), I'm not going. The pain is tiring. To be honest, I was just practicing out there for the Ryder Cup.'
Ryder Cuppers Padraig Harrington and Pierre Fulke both had final round 4-under 68s and ended in a tie for 14th.
Defending champion and four-time German Masters winner Bernhard Langer posted a 3-under 69 to finish in a tie for 10th at 15-under.
Final scores of the Linde German Masters