Holders Spain leapfrogged the Eastern Europeans to the top of Group C thanks to a 2-0 success in Oviedo but Costa again failed to score and has netted just one goal in eight appearances since opting last year to play for La Roja instead of his native Brazil.
The 26-year-old did win a penalty, converted by Andres Iniesta after Jordi Alba's early header, but otherwise struggled to make any impact on Slovakia's well-drilled defence before making way for Paco Alcacer 15 minutes from time.
"Of course I would like him to score but he did some good work," Del Bosque told a news conference.
"Against a team playing so defensively the player who has the most difficult job is the one in his position," he added.
"He moved well, he kept the defenders busy. We have to be patient. A lot of the time when he gets the ball he has his back to goal."
With seven of 10 matches played, Spain and Slovakia each have 18 points, with the Spanish, who lost 2-1 in Zilina in October, top due to a better head-to-head record.
Ukraine, who won 3-1 at home to Belarus earlier on Saturday and are assured of at least a playoff berth, are third on 15 points, 11 ahead of Belarus and Luxembourg.
The nine group winners and runners-up and best third-placed side qualify for the finals in France, while the eight remaining third-placed teams contest playoffs for the last four berths.
Spain travel to Skopje to play bottom side Macedonia in their next qualifier on Tuesday, when Slovakia host Ukraine.
Del Bosque criticised the fans at Oviedo's Carlos Tartiere stadium who whistled Spain's Barcelona centre back Gerard Pique throughout Saturday's match.
Some of those present were clearly fans of Barca's arch rivals Real Madrid and had objected to some playful remarks Pique recently made about the club.
"I find it disgraceful that there are people who whistle a national team player," Del Bosque said. "Gerard played fantastically well today."
(Writing by Iain Rogers, editing by Amlan Chakraborty)
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