Des Smyth of Ireland, who shared the lead with Ebihara after the second round, carded a 3-under 69 to finish alongside Jim Ahern at 12-under-par 204.
Ebihara exploded out of the gate with three straight birdies at the Rolling Oaks Course at World Woods Golf Club. Ebihara added two more birdies on the front side to make the turn at 14-under.
He added a birdie at the par-4 11th before the only bogey of his round at the 12th. The dropped shot was his first since the opening round, a span of 41 holes, and he recovered well with birdies at 14 and 16 to pad his lead.
'I'm very happy with this round. I haven't put two rounds together like this in quite awhile,' said Ebihara, who won the Order of Merit title on the European Senior Tour this year. 'I'm in good position but the key for me tomorrow will again be to get off to a good start. If I can do that, I think I'll be relaxed and the rest will take care of itself.'
Smyth had six birdies for his third straight round in the 60s, but he ran into trouble on several occasions resulting in three bogeys.
'I got off to a good start with those five birdies in the first seven holes and then those back-to-back bogeys just stopped my momentum,' said Smyth. 'I'll be in good shape, but I'll need to be nervous when I step on the first tee tomorrow. That's how I need to approach it.'
Ahern knocked his second shot to 18 feet at the par-5 third for an eagle to get his round going. He added six birdies and one bogey the rest of the way for a round of 65.
'I really played good all day,' said Ahern. 'My plan for the week was to not put any extra pressure on myself. I'm not going to do anything different tomorrow. I'll just go play my game and see what happens.'
Mike Smith, Mark Pfeil and Jerry McGee were seven shots off the lead at 9-under-par 207.
Former major league pitcher Rick Rhoden finished alongside Dave Barr and John Schroeder at 8-under-par 208.
Full-field scores from the Champions Tour Q-School Finals