Yorkshire carried on from their overnight total of 325-4 and Brophy went on to complete his century before he was caught by Ant Botha after Neil Carter picked up his fourth wicket of the innings when he had Rashid trapped lbw.
It was 369-7 when Rafiq was caught by Stefan Piolet. Forty five runs were put on by Pyrah who finished 45 not out and Patterson who was run out but Warwicks were able to mop up the tail and get Yorks all out for 425.
Things started well for Warwicks, who passed the one hundred run mark before Darren Maddy was out for 35 with the score on 102.
Ian Westwood who had contributed 66 runs to that partnership went two runs later. Botha and Jim Troughton added 44 before the Stratford born batsman was caught by Lyth.
Javid went for one and Botha was also caught by Lyth to leave Warwicks on 186-5 when the rain came down.