The Free State was the only province that broke the 90 percent threshold. It achieved an increase of 5.5 percent from the 87.7 percent the province achieved in 2015.
"I am so excited I could not believe it when I heard the numbers. I did not know that we achieved so much from last year's 87 percent...Free State has set the record," he told reporters in Johannesburg.
He thanked teachers, parents and subject advisers for helping the learners.
"I thank the whole community, we also had a strong backing from our community radio stations across the Free State. This is a very proud moment for us."
Motshekga congratulated Mekgoe, whose province beat the Western Cape for the top spot. The Western Cape was the best performing province in the 2015 with an 84.7 percent pass rate, followed by Gauteng at 84.2 percent.
"With all the challenges of public education and having to deal with learners from poor to wealthy households, children from rural and urban settings, learners facing a variety of problems, big learner numbers and just dealing with South Africa in its different manifestations...breaking this [90 percent] threshold is no child's play in the public sector."
Motshekga announced a national pass rate of 72.5 percent – up from the 70.7 percent in 2015.
The 2016 pass rate includes progressed learners – those who had failed Grade 11 twice and been pushed through to Grade 12.
Excluding the large cache of progressed learners, the pass rate was at 76.2 percent.
The Eastern Cape was the worst performer after achieving a 63.3 pass rate, an increase of 1.1 percent from 62.2 percent in 2015.
Limpopo followed with 68.2 percent, a decline of 3.5 percent from 71.7 percent in 2015.
Western Cape came second and trailed behind Free State with an 87.7 percent, a decline of 0.3 percent from 88 percent in 2015.
Gauteng followed at third place after achieving 87 percent, an increase of 1.1 percent from 85.9 percent in 2015.