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Two tries by winger Daishi Murata and one from Samoan utility back Tusi Pisi helped Suntory extend their unbeaten run to 21 matches at a packed Prince Chichibu Memorial Rugby Ground, but it was the 32-year-old former Wallaby captain who stole the show.
Suntory were twice reduced to 14-men when Murata and then South African World Cup-winning scrumhalf Fourie du Preez were sin-binned but Smith made up for the numerical disadvantage much to the relief of his coach.
"It was a difficult time," Suntory coach Okubo said of the yellow cards. "But we had George. He can pass as well be a presence at the scrums and lineouts."
Quick thinking by the canny Du Preez set Murata free to score in the corner after only eight minutes of the grand final before English flyhalf David Hill reduced the deficit to 5-3 with a penalty.
Murata was again the beneficiary of a team mate's shrewd play when he collected a cross kick from flyhalf Kosei Ono to score his second try in the 34th minute. New Zealand centre Nicholas Ryan added the conversion to make it 12-3 at halftime.
Murata was sent to the sin bin at the start of the second half after one of many Suntory infringements, with Du Preez following him 20 minutes later but Toshiba could not breach the Suntory defence, marshalled expertly by Smith.
Replacement Pisi then sealed the win with Suntory's third try after the champions forced a turnover deep in their own half.
"We just couldn't seem to get our attack going in the first half," Toshiba coach Kenichi Wada was quoted as saying by Kyodo.
"Suntory's defence was very good. Though we let them play to their strengths."
Suntory won all 13 matches in the regular season before dispatching South African centre Jaque Fourie's Kobe Steel Kobelco Steelers in the semi-finals.
Five-times champions Toshiba finished second in the league campaign and reached the final with a playoff win over Panasonic Wild Knights, who signed All Black World Cup-winning centre Sonny Bill Williams for part of their campaign.
Suntory's victory was their third Top League title after their 2007-08 success.
"We believed in ourselves and in our rugby and that gave us this result," Suntory captain Shinya Makabe said.