PSV Eindhoven centre-back Bouma had to be substituted after a collision in the first minute when he and defensive colleague Johnny Heitinga clashed heads. Feyenoord's Ron Vlaar was Bouma's replacement, while Heitinga was comfortable enough to stay on the pitch.
Ibrahim Afellay helped to put Holland in front after seven minutes when the Barcelona forward, who returned to action only last month after a serious knee injury, produced a tricky run along the left and his low cross prompted Slovakia defender Kornel Salata to put the ball into his own goal.
After defeats to Bayern Munich and Bulgaria, Holland were seeking a confidence-boosting win ahead of their European Championship campaign.
Robin van Persie fired a shot over the crossbar but was mostly kept quiet by Slovakia around the penalty area, and Klaas Jan Huntelaar came off the bench to replace the Arsenal man midway through the second half.
Sneijder had already gone off by that stage, the Inter Milan playmaker suffering an ankle knock in the 51st minute, with Holland boss Bert van Marwijk wanting to take no further risk with such a key player.
Rafael van der Vaart doubled Holland's lead after 75 minutes with a precise low right-footed shot from 15 yards across goalkeeper Jan Mucha and into the left corner.
Afellay made way for Dirk Kuyt late on, while Luciano Narsingh was brought on in place of Arjen Robben for an international debut.
Holland complete their match preparation for Euro 2012 when they play Northern Ireland in Amsterdam on Saturday.