On February 2, 2010, Mota signed a minor league contract with the San Francisco Giants with an invitation to spring training, marking the first time he was a non-roster invitee. On April 4, he was placed in the final spot in the Giants' bullpen. He started his tenure with the Giants with nine consecutive scoreless outings. On May 5, he got his only save of 2010 in a 9–6 victory over Florida. Mota took over the setup role in May, but lost it after allowing five runs and losing one of three games from June 10 to 13. He compiled a 1.27 ERA over his first 23 games, but a 7.48 ERA over his next 28 games raised his ERA to 4.78. On July 4, he intentionally walked four batters in innings (due to runners reaching third base with nobody out in the 14th and 15th innings) and was the losing pitcher when he allowed a run in the 15th inning of a 4–3 loss to Colorado. On August 23, he was placed on the disabled list with iliotibial band syndrome to make room for Cody Ross on the Giants' roster. He returned to the Giants on September 6. Mota did not give up an earned run in his final five appearances of the season to finish the year with a 1–3 record and a 4.33 ERA in 56 games, and he made the Giants' playoff roster as they won the NL West. However, he was not used until Game 2 of the 2010 World Series, when he pitched a scoreless ninth inning in a 9–0 victory over the Texas Rangers. His only other postseason appearance came when he pitched scoreless innings in a 4–2 loss in Game 3. However, Mota won his first World Series when the Giants defeated Texas 4 games to 1 in the series. After the series, he filed for free agency.