Holcomb's crew finished sixth in the season standings.
Melbardis, Daumants Drieskens, Arvis Vikaste and Arvis Dambis had a two-run time of 1 minute, 52.29 seconds to edge Thomas Florschuetz's German team by 0.02 seconds.
Zubkov was tied for third with Russia's Alexander Kasyanov, 0.14 seconds behind the winner at Sanki Sliding Centre.
Zubkov, who also won back-to-back overall titles in 2005-06, won five races this season to total 1,727 points from eight events. Melbardis was second with 1,625, followed by Gemany's Manuel Machata with 1,594 points.
Holcomb, Justin Olsen, Steven Langton and Curtis Tomasevicz finished in 1:53.10.
Dutch speedskater Sven Kramer has become the first man to win six allround world championships. Kramer secured his sixth victory by taking the final 10,000-meter race in Hamar, Norway, clocking 13 minutes, 1.86 seconds to beat Belgium's Bart Swings and Havard Bokko of Norway.
Bokko, Kramer's main rival, won the opening 1,500 race in 1:46.34, beating Poland's Zbigniew Brodka and Swings. But Kramer was only 0.41 seconds back in fourth to keep an edge in the overall standings and finished with 149.228 points. Bokko was second with 149.447 and Swings third with 149.800.Ireen Wust of the Netherlands won both the 1,500 and 5,000 races Sunday to secure her fourth women's title with 161.530 points. Countrywoman Diane Valkenburg was second with 163.120 points and Russia's Yekaterina Shikhova was third with 163.444.
Japanese teenager Sara Takanashi earned her second victory in two days at a women's ski jump World Cup meet in Ljubno, Slovenia, dominating a normal hill event.
The 16-year-old Takanashi had the longest jumps in both rounds, clearing 97 and 100 yards to win with 266.9 points. Coline Mattel of France was a distant second with 243.3 points, ahead of Park City's Sarah Hendrickson at 241.8.
Takanashi extended her already large lead in the overall World Cup standings. She has 1,137 points, with Hendrickson second at 847. Mattel is third with 733.
Takanashi also won Saturday's event, ahead of Hendrickson.