The Insect Science rider crossed the line in 3:23:30 to finish 20 seconds ahead of Gordon on day two.
CP van Wyk, who also rides for Insect Science, completed the podium.
Gordon’s performance was good enough to wrest the overall lead from stage one winner Andreas Kuhn, who placed around nine minutes down in fourth.
His total time of 5:57:36 puts him just over three minutes ahead of Van Wyk (6:00:42) in the general classification with one stage to go.
Bontekoning is third in the standings on 6:02:08.
Sarah Hill (Galileo Risk) claimed her second stage victory on the trot to take a comfortable lead into the final day.