Del Bosque, who said on Friday he had agreed to stay on until 2016, fielded a host of reserve players for the match in Malabo but Spain were still comfortably better than their former African colony, ranked 119th in the world.
A howler from home goalkeeper Danilo gifted the world and European champions their opening goal in the 13th minute when he dropped a Juan Mata centre and Santi Cazorla tapped into an empty net.
Defender Jimmy Bermudez levelled with a fine header from a corner in the 36th minute before Juanfran lashed in a loose ball from close range two minutes before halftime.
Bermudez celebrated wildly after rising unmarked to power the ball past Pepe Reina and Spanish media reported the Equatorial Guinea players had been promised a 50,000-euro ($67,400) bonus if they scored.
Spain's victory, their 68th in 83 matches under Del Bosque, was soured by an injury to midfielder Alonso, who was making his first appearance for his country after five months out following surgery on a groin problem and a broken toe.
One of several Spain players on the receiving end of some wild tackles from their opponents, many of whom play in Spain's lower leagues, Alonso hobbled off and was replaced by Sergio Busquets shortly before the break.
The Spanish soccer federation (RFEF) said the Real Madrid player had suffered a bruised ankle, suggesting he may be unavailable for Tuesday's friendly against South Africa at Soccer City in Johannesburg, the scene of Spain's maiden World Cup triumph in 2010.
"They were physically very powerful and they did not allow us to play within our comfort zone," Del Bosque said in a pitchside interview with Spanish TV broadcaster Telecinco.
"We didn't get drawn into the battle and tried to play our game and we missed a few scoring chances," he added.
Marc Bartra of Barcelona made an accomplished debut alongside Real Sociedad's Inigo Martinez in central defence, while Napoli's Reina made a rare appearance in goal with captain Iker Casillas and Victor Valdes on the bench.
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