The Iveco man won by just over a minute from the Czech Republic's Ales Loprais.
He was boosted by problems suffered by his fellow Dutchman Hans Stacey, who lost 25 minutes after tipping his truck over.
Stage Two result
1 - Gerard de Rooy (NED) - 3:00:59
2 - Ales Loprais (CZE) - 3:02:00 +01:01
3 - Miki Biasion (ITA) - 3:08:51 +07:52
4 - Martin Kolomy (CZE) - 3:17:15 +16:16
5 - Pieter Versluis (NED) - 3:19:36 +18:37
6 - Eduard Nikolaev (RUS) - 3:19:37 +18:38
7 - Hans Stacey (NED) - 3:26:05 +25:06
8 - Ayrat Mardeev (RUS) - 3:27:29 +26:30
9 - Jaroslav Valtr (CZE) - 3:27:58 +26:59
10 - Martin van den Brink (NED) - 3:28:54 +27:55
