Paul Casey, Harrington's teammate on the Ryder Cup, finished two shots off the pace at Gut Lrchenhof along with Raphael Jacquelin, Nick O'Hern, Richard Green, Greg Owen and Louis Oosthuizen at 4-under-par 68.
After a trio of European Ryder Cuppers put together strong showings last week at the European Masters, Harrington, the top-ranked European player in the world, continued to showcase the potential of the European team with the Ryder Cup one week away.
'Obviously, you come here as a warm up. One eye is definitely on next week,' Harrington. 'But once you're in contention, it's this week you're thinking about.'
The Irishman picked up back-to-back birdies from the second and added two straight birdies starting at the par-4 10th to reach 4 under. After a bogey at the 13th, Harrington dropped his second shot inside 7 feet and converted the putt for birdie at the 14th.
Harrington then birdied the par-4 15th to move to the top of the leaderboard and broke a tie with Cejka thanks to a long birdie at the par-4 17th. Harrington had another birdie chance at the last after his approach stopped within 12 feet of the hole, but his putt just missed the left edge of the cup.
'I really enjoyed that round,' said Harrington, who missed the cut at the BMW International Open, his last start on the European Tour. 'The way things have been going the last couple of rounds I've been getting a bit bogged down on myself. Today was a lot better, I was a lot easier on myself.'
Cejka jumped out of the gate with birdies on each of his first three holes. He found trouble with a bogey at the sixth, but was able to recover on the inward half with another string of birdies.
The German drained a 12-footer for a birdie at the 12th and ran home a 5-foot putt for a birdie at the par-5 13th to move to minus-4. Cejka then birdied the par-5 15th to take second place along after a round of 67.
Casey played the back side first and was on fire early with three consecutive birdies starting at the par-4 12th. He stumbled to a double bogey at the 18th, however, but countered with a birdie at the very next hole.
The 27-year-old hit his third to 15 feet for a birdie at the par-5 seventh and sank a long birdie putt at the eighth to finish in a tie for third.
'The rough this week is thick, it's a lot thicker than it's ever been here before,' said Casey. 'If you don't drive the ball well you're going to struggle.'
Barry Lane, Graeme McDowell, Jose Maria Olazabal, Anthony Wall, Gary Murphy and Rolf Muntz shared ninth place at 3-under-par 69.
K.J. Choi, who became the first Korean to win on the European Tour when he captured this event last year, carded a 1-under 71 to finish five shots back in a group that included Darren Clarke.
Ryder Cup captain Bernhard Langer joined Colin Montgomerie in a group at 1-over-par 73.