Yes, but radio reception is not as good if you only plug in the large lead. Quote below-
"The Scion head unit only has one antenna input. There is a piece of metal covering the second input. When I installed my Scion radio, I cut off the small piece of metal, and was able to plug both antenna cable into the head unit. Both 4Runner antenna cables do plug into the Scion head unit.
However, this does not improve reception, since the Scion head unit does not use the second antenna input. It is a dead end, inside the box. This means that radio reception is slightly better with the original head unit. But it also means that your 2nd antenna cable is not loose behind the dash.
BUT: AM or FM sound quality isn't as good as CD or MP3 or iPod anyway. In my mind, it was no great loss. We still listen to FM around town, with no problems."