The American rapper was visibly moved when he asked the thousands of festival goers to light up Weston Park as he performed Encore/Numb - a song from his collaboration EP Collision Course with Linkin Park.
Linkin Park singer Bennington died earlier this year, with the band performing their last ever live show in Birmingham.
The tribute came close to the end of Jay-Z's set on the main stage.
A monster balloon modelling animal filled the stage as Jay-Z made his arrival to the screams of the crowd.
He told them it was the first ever performance of his new album, 4:44 and asked them to bear with them as the band dealt with any teething problems.
The album sees the controversial rapper baring his soul about his past, from apologising for his infidelity to his wish to leave a legacy to his children; and even his views of OJ Simpson.
But those tracks were appreciated mostly by hardcore Jay-Z fans who have the album.
The majority of the crowd wanted to hear the hits such as 99 Problems, Empire State of Mind and Holy Grail and Jay-Z obliged to the crowd's delight.
It was, however, a huge shame the two best sets on the Saturday clashed.
On the other side of the park, dance fans were entranced by a fabulous gig from Pete Tong and the Heritage Orchestra.
Many dipped in and out of both venues torn between seeing the best dance tracks played by a real orchestra with a laser show holograms - and one of the biggest names in the music world.