Abraham Papali'i and Shane Delahunt were sent off in the second half and Munster capitalised to move into the last four of the Pro14.
New Munster signing RG Snyman faces a long spell on the sidelines after the Pro14 club confirmed he has torn his anterior-cruciate ligament.
Leinster picked up where they left off in the Pro14 as they held off Munster in a thrilling contest in Dublin on Saturday.
Leinster became the first Pro14 side to win their first 12 league matches of a season after they overcame Ospreys on Friday.
It was a record-breaking outing for Munster in Pro14 action on Friday, while Glasgow Warriors were also big winners.
At the end of another week of crisis, Saracens had rare cause for cheer as they reached the quarter-finals of the European Champions Cup.
A thrashing of Lyon ensured Leinster made it five wins from five in the European Champions Cup, while Racing 92 reached the last eight.
Joey Carbery has suffered another injury blow and will play no part in Ireland's bid to regain the Six Nations title.
Ulster maintained their unbeaten home record in the Pro14 with an emphatic win over Munster, who slipped off the top of Conference B.
George Turner's late try ensured Glasgow Warriors claimed the bragging rights in their 1872 Cup clash with Edinburgh in the Pro14.
Saracens claim a derogatory comment made to Jamie George by Munster's chief medic sparked a fracas at Allianz Park.
There were seven tries in Leinster's 43-16 European Champions Cup win over Northampton Saints as they made it 10 victories from 10.
Eroni Sau's try proved decisive as Edinburgh saw off Pro14 Group B leaders Munster, while Ulster thrashed Scarlets on Friday.
Munster were delighted to have Andrew Conway back in Pro14 action as he settled an all-Irish affair with Ulster.
After succumbing to a thrashing against Edinburgh in their previous match, Scarlets narrowly beat Cheetahs in Pro14.
Munster top Pro14 Conference B after their 28-12 victory over Ospreys, while Cardiff Blues were defeated 23-14 by Ulster.