On September 1, Mota was the winning pitcher when he pitched a scoreless inning in an 8–7 victory over Houston. He got another win by pitching a scoreless inning on September 12 in a 6–4 victory over Florida. With the Mets, he had a 3–0 record with a 1.00 ERA and 19 strikeouts in 18 games to finish the season 4–3 with a 4.53 ERA in 52 games. He made the playoffs for the first time in his career as the Mets won the NL East. In the first game of the 2006 National League Division Series against the Dodgers, Mota was the winning pitcher when he pitched two innings, although he blew a 4–1 lead by giving up three runs and allowing the Dodgers to tie the game. Mota pitched two scoreless innings in the Mets' series-winning 9–5 victory over the Dodgers in Game 3. In the 2006 National League Championship Series, Mota appeared in five of the seven games in the series. He blew a lead in an eventual Game 2 loss, but he did not give up a run in the other four games as the Mets lost to St. Louis in seven games. On October 30, he filed for free agency.