Santi Cazorla and Juanfran scored for a second-string Spain side to help the reigning world and European champions to victory in Malabo.
Jimmy Bermudez had equalised for the hosts on 36 minutes, but the visitors never looked like losing despite failing to build on their one-goal advantage.
Del Bosque praised Equatorial Guinea, who are ranked 119th in the world, for making it hard for his team.
"It was an awkward match for us," he told reporters.
"They were physically strong and did not let us play.
"We have wanted to play our game, but often we were inhibited."
In his first appearance for the national team since March, Xabi Alonso came off late in the first half with what appeared to be an ankle injury.
Del Bosque said the substitution was just a precaution and played down the seriousness of the injury.
"Xabi was brought off just as a precaution," he said.
"It's nothing serious – just a knock."
