The 2011 world road race champion, who is hoping to negotiate an amicable split from the successful British team, had suffered a crash in the closing stages of the opening round and finished second best in a dash for the line at Knowsley Safari Park yesterday.
However, after the peleton - lead by Team Sky colleagues Jeremy Hunt and Tour de France winner Bradley Wiggins - had finally reeled in the breakaway group heading into the final two kilometres, the Manx Missile was not to be denied as he sprinted clear.
At one stage of the 152km route, which had started in Jedburgh, a breakaway group of IG's Peter Hawkins, Raleigh's Bernard Sulzberger, Kristian House of Rapha Condor, Peter Williams of Node4-Giordana Racing and Vacansoleil's Wesley Kreder opened up an advantage of around four minutes on the peleton.
However, as the course, which raced through changeable conditions, weaved back into the final lap of Dumfries, that was slowly eaten away.
Garmin's Sep Vanmarcke did his best to support Kreder but the pair were eventually caught inside the last two kilometres as the finish along White Sands came into view.
Team Sky's Luke Rowe, who had avoided the carnage at the end of stage one in Norwich to claim his first professional stage win at the Royal Norfolk Showground, then provided the perfect lead up for Cavendish to take the line ahead of Leigh Howard of Orica-GreenEdge.
Cavendish said on ITV4: "The finish was downhill so I knew I could go pretty early and had the perfect lead out.
"Luke was so fast at the end, Berny (Bernhard Eisel) before him, and Brad also kept them strung out.
"It was pretty text book."
Second place was enough for Australian Howard, who won yesterday, to claim the IG Gold jersey with Aidis Kruopis of Orica third and Rowe in fourth this afternoon.
The Tour of Britain heads to Carlisle on Wednesday for a 156km race down to Blackpool.
Should Cavendish again perform well, the Manxman could himself move into contention for the overall Tour lead.
However, he said: "I had done it before and am wearing the world champion's jersey and only have a couple more days, so would like to savour that more than anything."