The Russian, who started out his Dakar career as a mechanic, lead a 1-2-3 by his compatriots and team-mates racing for the all-conquering Kamaz team, with Ayrat Mardeev coming second and Andrey Karginov coming third.
Pieter Versluis won the final stage of the race to take the first Dakar stage victory of his career by two minutes four seconds from defending truck champion Gerard de Rooy.
De Rooy went into the final day with hopes of making the podium, but though he made up over five minutes on Karginov he was still four minutes adrift in fourth place overall.
"It hasn't sunk in yet! I'm full of emotions because, after fighting minute by minute, second by second, throughout fifteen days of racing, I've finally made it, I've won the Dakar," said Nikolaev.
"It's simply incredible! I'm on cloud nine. For me, it's a dream come true, a dream which began five years ago when I got into a racing Kamaz for the first time as a mere mechanic. I dreamed of winning this rally someday and I did it! I still can't believe it happened!"
Stage 14 truck results
1 Pieter Versluis (NED) 2:02:40
2 Gerard de Rooy (NED) 2:04:44 +02:04
3 Miki Biasion (ITA) 2:04:57 +02:17
4 Ales Loprais (CZE) 2:04:59 +02:19
5 Ayrat Mardeev (RUS) 2:05:19 +02:39
6 Martin Kolomy (CZE) 2:05:52 +03:12
7 Eduard Nikolaev (RUS) 2:08:36 +05:56
8 Andrey Karginov (RUS) 2:10:09 +07:29
9 Marcel van Vliet (NED) 2:10:53 +08:13
10 Frits van Eerd (NED) 2:11:18 +08:38
1 Eduard Nikolaev 39:41:43
2 Ayrat Mardeev + 37:10 +
3 Andrey Karginov + 37:57 +
4 Gerard de Rooy + 41:16 +
5 Martin Kolomy + 1:01:47 +
6 Ales Loprais + 1:16:10 +
7 Pieter Versluis + 2:32:09 +
8 Marcel van Vliet + 3:22:13 +
9 René Kuipers + 3:53:50 +
10 Pieter van den Bosch + 4:23:52 +