An unfortunate Nicolas Hofler own goal gave the hosts the lead before a Jefferson Farfan penalty made sure of victory for the Royal Blues, who reached the last 16 of the Champions League on Wednesday.
The game also marked the return to action of former Liverpool target Kyriakos Papadopoulos after over a year out with a knee injury.
Freiburg made a bright start to the game and Karim Guede had two good early opportunities.
Schalke spent much of the first half chasing the ball and had to wait over half an hour before testing Freiburg goalkeeper Oliver Baumann.
Felipe Santana should probably have done better too as his shot from close range struck the goalkeeper on his shoulder, bouncing away to safety.
The hosts took the lead two minutes before half time when a Farfan corner was diverted into his own goal by Hofler, who was not under any pressure at the far post.
Freiburg responded well early in the second half and nearly levelled when Matthias Ginter's header only just missed the right- hand upright.
Schalke then took control of the situation and Max Meyer nearly beat Baumann with an acrobatic overhead kick which the Freiburg goalkeeper tipped over the crossbar.
Just a minute later, Meyer went to ground as he entered the penalty area, and a spot-kick was given.
Farfan stepped up to send Baumann the wrong way and become Schalke's top scorer this season with six goals.
There was time for Schalke coach Jens Keller to give both Farfan and Papadopoulos a standing ovation as the Greek defender replaced the Peruvian forward for the final four minutes, making his return to action for the first time since suffering a serious knee injury in November 2012.