The director told SFX that the studio wouldn't have given him the greenlight for the sequel if he refused to meet their demands.
"The studio said, 'You have to make it in 3D if you're going to make it, for economic reasons'," Abrams said. "But my feeling was I didn't like 3D. So the idea of doing Star Trek in 3D was ridiculous.
"But that was very helpful in some ways, because it let us work with stereographers and the 3D crew in a way that didn't assume we just loved 3D."
Abrams admitted that he approached the 3D post-conversion "very cynically", but was eventually won over by the process.
"I have trouble with 3D sometimes. I can't see it right; I get a headache; it annoys me; I hate the glasses; I hate the fact that things get so dim," he explained.
"I approached it very cynically. And the fact is that we've been using techniques that haven't been used before in 3D. They've figured out things. They've made enough movies now with this new process that they can understand ways to eliminate some of these problems.
"Things like breaking shots into zones, 3D zones, using multiple virtual cameras. A lot of this has made me a believer, whereas before I was really against it… There's this myth that if you don't shoot the movie in 3D it doesn't look good. Actually, the opposite can be true."
Abrams added that he believes the 3D in Star Trek Into Darkness won't be detrimental to the finished film.
"The key for me is I got to make my 2D movie that I wanted to make, just the way I wanted to; and it gets to be augmented in 3D but that doesn't detract from the 2D," he commented.
Star Trek Into Darkness, starring Chris Pine, Benedict Cumberbatch, Alice Eve and Zachary Quinto, will open in cinemas on May 17.
Photo gallery - Star Trek Into Darkness in pictures: