Nishikori, who won his third career title at The Racquet Club last year, will play Russian Alex Bogomolov Jr. in the quarterfinals Friday. Bogomolov beat American Ryan Harrison 6-3, 2-6, 6-2 earlier Wednesday.
The defending champ started slowly as he struggled a bit with his serve. Nishikori, who didn't drop a set here winning this tournament a year ago, jumped out to a 3-1 lead only to be broken twice. Nishikori broke Becker to open the match and again after the German broke him for a second time to tie the set at 4-4.
''You see the score it looks simple like easy,'' Nishikori said. ''But with so many breaks and I was serving all right but a couple moments I wasn't feeling the ball and the ball was going everywhere. So I led in unforced errors I guess today. First match and never easy of course against Becker, but I'm happy to win two sets today.''
American Jack Sock beat Jiri Vesely of the Czech Republic 6-2, 6-1. Sock needed 68 minutes to top Vesely overcoming six double-faults on his way to his second quarterfinal this year. Michael Russell downed fellow American Tim Smyczek 6-2, 7-6 (5) and will play third-seeded Lleyton Hewitt of Australia or Marcos Baghdatis of Cyprus.
Qualifier Denis Kudla beat fellow American Donald Young 6-1 6-1 in a first-round match needing only an hour to get a little payback for losing to Young here last year.
Nishikori, ranked as high as No. 11 last June, is trying to successfully defend a title for the first time in his career. He also is playing as the top seed at an ATP Tour event for the first time this week.
''It's a weird feeling actually,'' Nishikori said about being the No. 1 seed. ''Especially I was playing without seed and now I'm top 20. And yeah, I didn't really feel like first seed. I didn't really care much, but it's a ... pleasure to be No. 1 seed.''
He started well enough breaking Becker to jump out to a 3-1 lead. Then he struggled as Becker broke him twice. Nishikori broke Becker's serve for the third time in going up 5-4 and served out for the set.
He won all three break points on Becker's serve. The German had seven break points on Nishikori and converted only twice in the opening set.
In the second set, Nishikori was much more in control. He jumped out to a 4-2 lead and was up 4-3 when Becker broke his serve. Nishikori broke right back and served out for the match and a win he was happy to take. Nishikori said his serve was much better in the second, though he wasn't happy with being broken.
''I was up 4-3. That's an important game,'' Nishikori said. ''I should finish well, but second set much better.''