The visitors had a chance to break the deadlock inside the opening two minutes as Chris Gunter burst forward down the right, but he could not connect with his shot well enough, giving Ferran Pol an easy save.
The hosts made a little slice of history in the sixth minute, taking the lead in a European Championships qualifier for the first time ever courtesy of an Ildefons Lima penalty.
It was Neil Taylor who conceded the spot kick, pulling Ivan Lorenzo down inside the area. Lima stepped up and sent Wayne Hennessey the wrong way to score his side's first goal in a competitive fixture for four years.
Bale was proving to be Wales' most dangerous player, but he couldn't quite rise high enough to connect with a Chester cross shortly before half time as the two sides went into the break all square.