The setback was the 10th straight for the Tigers, who ended their season with a 22-34 overall record and a 9-21 mark in the SEC.
Arkansas clinched the fourth seed for the SEC Baseball Tournament next week in Hoover as the Razorbacks finished the regular season 18-12 in the conference and 38-17 overall.
As was the case in the first two games of the series, the Tigers didn't get a good performance from the starting pitcher. On Saturday junior Chris Dennis lasted only four innings. He have up seven hits and seven runs, six which were earned.
However, as they had done in earlier games, the 15th-ranked Razorbacks matched and trumped the Tigers. This time it was with two runs in the bottom of the second inning, two more in the second and three runs in the fourth inning plus three more in the fifth.
Brian Walker, who had hit two homers earlier in the series, gave the Razorbacks the lead for good with a two-run homer in the second.
The Razorbacks used the long ball in the third inning to increase the lead on back-to-back home runs from Danny Hamblin and David Hum.
Auburn didn't score again until adding a run in the sixth inning. Freshman catcher Ryan Jenkins, who had three hits, singled home Sain, who had walked earlier in the inning.
Arkansas added an insurance run in the seventh inning to regain its nine-run lead.
Auburn finished with 11 hits, just one fewer than the Razorbacks, but the Tigers left 15 runners on base.
Arkansas did a better job of making the hits count, especially Jake Dugger, who drove home five RBI on two hits to the delight of a crowd of 8,425.
Shaun Seibert was the winning pitcher. He gave up just five hits and one run in five innings to improve his record to 4-0 while Dennis fell to 3-7.
Auburn's Peter Wiggins gave up three runs, two which were earned, in one inning of relief.
Byran Woodall pitched 2 2/3 innings and allowed three hits and one run for the Tigers.
Senior Grant Cardwell wrapped up his AU career by pitching one-third of an inning without allowing a run.
In addition to Sain, Johnstone and Cardwell, it was the final game for senior Jeff Boutwell, who was 0-4 at the plate.