Replying to Gujarat's 244, Mumbai ended the day two at a solid 323 for five with Suryakumar Yadav (23) and Aditya Nayar (6) at the crease.
Jaffer, who was six overnight, batted superbly almost all day as Gujarat managed just three wickets today.
Jaffer's 171 came off 271 balls with the help of 21 fours and a six.
Jaffer lost partner Aditya Tare (20) early but found good support from Hiken Shah (82) as the two added 213 runs for the third wicket.
The partnership was broken by Samit Gohel when he castled Shah, who faced 186 balls and hit 10 boundaries in his 82-run knock.
Left-arm paceman Rush Kalaria denied Jaffer a double century as he had the Mumbai opener caught by Gohel in the fag end of the day.
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Kalaria also sent packing Nikhil Patil, who could not even open his account.
Brief Scores:
Gujarat 1st innings: 244 all out
Mumbai 1st innigs 232 for seven in 99 overs. (Wasim Jaffer 171, Hiken Shah 82; Rush Kalaria 2/48).