Jaffer scored a patient knock of 132 when other top order batsmen failed but Mumbai had enough useful partnerships to pile up 287 for 6 to take a 139-run lead.
Jaffer now has became the highest run-scorer in the history of Ranji trophy as he left behind Amol Muzumdar, whose tally stood at 9105.
Jaffer needed 83 to cross Muzumdar's mark and after today's innings his total is 9155. He also eclipsed Ajay Sharma's record of 31 centuries in the championship.
Jaffer's knock contained 16 fours and a six in 246 balls.
There was a brief period after tea when Saurashtra looked to be fighting their way back by taking three quick wickets