Australia's Fabrice Lapierre took gold while former world medallist Ignaisious Gaisah completed the podium.
Rutherford missed the European Championships in Barcelona with a foot injury but this performance certainly made amends, with an 8.22m season's best adding extra gloss.
However, Chris Tomlinson - whose participation was in doubt after picking up an ankle injury in qualifying - recorded three no jumps in the final and certainly looked short of full fitness.
"It's been a long time coming and it feels great," said British record holder Rutherford, who won his last silver medal at the 2006 European Championships in Gothenburg.
"There were still a few technical issues which probably cost me the gold but I'm delighted to be back on the podium, it's been four long years.
"It shows me that I can produce the goods when it matters and that is a big confidence boost going into the winter.
"This was a quality field and I really believed the gold could have been out there for me but I've no complaints, I'm very happy."
Elsewhere, England's Samson Oni and Tom Parsons were fourth and fifth in a men's high jump final won by Bahamas' Donald Thomas with a 2.32m season's best.
New Zealand's Valerie Adams defended her Commonwealth shot title - adding Delhi gold to her Olympic and world title - with a Games record 20.47m best effort.
Trinidad's Cleopatra Brown and Samoa's Tasele Satupai completed the podium while Rebecca Peake was the pick of the British athletes in fifth.
South Africa's Sunette Viljeon claimed the women's javelin title but England's Laura Whittingham just missed out on a medal in fourth and international newcomer Izzy Jeffs was well off her best, finishing 13th.
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