Bernard claimed a late victory after passing EF's Michael Woods and Freddy Ovett of Israel Start-Up Nation, with French rider Bernard winning by using a late power-up.
NTT retain the lead in the overall competition and will have the maillot jaune for stage three, which will take place next weekend. The King of the Mountains competition is led by Israel Start-Up Nation.
Impressive Ganna tops opening Giro TT in Turin
Julien Bernard wins dramatic Stage 2 of Virtual Tour de France
Both the men's and the women's events ran over a 29.5km route with two climb sections.
There was also late drama in the women's section, with the American rider Stephens recovering from dropping back on the course's main ascent. Joscelin Lowden of the Drops team came in second, with Ceratizit-WNT Pro Cycling Team taking the last podium spot.
There are four stages of the virtual Tour remaining, with Tibco-Silicon Valley Bank taking the leader's jersey for now, while Canyon-SRAM have the Green jersey.
'So close!' - Lauren Stephens triumphs on Stage 2 of Virtual Tour de France
1 Julian Bernard (Fra) Trek-Segafredo 0:41:12
2 Freddy Ovett (GBr) Israel Start-Up Nation
3 Nicolas Edet (Fra) Cofidis
4 Michael Woods (Can) EF Pro Cycling
5 Patrick Bevin (NZl) CCC Team 0:00:01
6 Stefan De Bod (Saf) NTT Pro Cycling 0:00:02
7 Giulio Ciccone (Ita) Trek-Segafredo
8 Louis Meintjes (Saf) NTT Pro Cycling
9 Tao Geoghegan Hart (GBr) Team Ineos
10 Gianni Veremeersch (Bel) Alpecin-Fenix
1 Lauren Stephens (USA) Tibco-Silicon Valley Bank 0:47:32
2 Joscelin Lowden (GBr) Drops
3 Enrica Magnaldi (Ita) Ceratizit-WNT
4 Cecilie Uttrup Ludwig (Den) FDJ Nouvelle-Aquitaine Futuroscope
5 Kristen Faulkner (USA) Tibco-Silicon Valley Bank
6 Pauliena Rooijakkers (Ned) CCC-Liv 0:00:15
7 Sarah Gigante (Aus) Tibco-Silicon Valley Bank
8 Ella Harris (NZl) Canyon-SRAM
9 Anna Henderson (GBr) Team Sunweb
10 Krista Doebel-Hickok (USA) Rally Cycling
Tour de Romandie
Thomas back to winning ways as blistering TT delivers Romandie GC title
Tour de Romandie
'I feel like a right whopper' - Thomas explains cause of bizarre crash