Matthews also showed himself, in the yellow jersey, and was sat fourth wheel under the flamme rouge as Orica-GreenEDGE upped the pace further.
Geraint Thomas was also prominent near the front – his aim being safety overall – but Etixx-QuickStep and Kittel were nowhere to be seen.
He was not alone though, as Bouhanni and Matthews led out the sprint, with Niccolo Bonifazio (Trek-Segafredo) on his wheel.
Bouhanni held the advantage, with Matthews seemingly boxed in and looking to use the smallest of gaps on the barriers to nip in ahead of the Frenchman.
Nacer Bouhanni was penalised for irregular sprinting (pic: ASO)
The Cofidis man closed the gap, however, and as both went shoulder-to-shoulder nearly took each other out – staying upright more by luck than design.
It prompted an angry reaction from the Australian as he crossed the finish line, with Bouhanni responding similarly.
Alexander Kristoff (Katusha) crossed in fourth place, a full second’s gap behind the three front-runners, but it was all eyes on the commissaires’ decision.
And though Bouhanni was interviewed immediately post-race as stage winner, it quickly became apparent Matthews would be handed his second stage win instead.
Paris-Nice 2016: stage two – result
1) Michael Matthews (AUS) – Orica-GreenEDGE – 5.04.26hrs
2) Niccolo Bonifazio (ITA) – Trek-Segafredo – ST
3) Nacer Bouhanni (FRA) – Cofidis
4) Alexander Kristoff (NOR) – Katusha +1”
5) Arnaud Demare (FRA) – FDJ – ST
6) Ben Swift (GBR) – Team Sky
7) Andre Greipel (GER) – Lotto-FixAll
8) Wouter Wippert (NED) – Cannondale
9) Adrien Petit (FRA) – Direct Energie
10) Jonas van Genechten (BEL) – IAM Cycling General classification
1) Michael Matthews (AUS) – Orica-GreenEDGE – 9.41.46hrs
2) Tom Dumoulin (NED) – Giant-Alpecin +14”
3) Patrick Bevin (NZL) – Cannondale +19”
4) Ion Izagirre (ESP) – Movistar – ST
5) Geraint Thomas (GBR) – Team Sky
6) Lieuwe Westra (NED) – Astana +24”
7) Dries Devenyns (BEL) – IAM Cycling +25”
8) Arnaud Demare (FRA) – FDJ – ST
9) Rafal Majka (POL) – Tinkoff +27”
10) Richie Porte (AUS) – BMC Racing – ST