After the 2000 season, Ramírez signed with the Yakult Swallows and was their cleanup hitter. During his final season with the Swallows he set the Central League record for most base hits in a single season with 204. The 2007 season, however, proved to be Ramírez's last with the Swallows, who did offer him the multi-year contract he sought. Instead, the outfielder signed with the Yomiuri Giants for the 2008 season. Ramírez quickly flourished with his new team. In 2008, he led the Central League with 125 RBI while hitting.319 with 45 home runs. He also hit two home runs in Game 2 of the Japan Series, including one in the bottom of the ninth to win Game 2. At the end of the 2008 season, Ramírez won the Central League MVP Award. He was the third Venezuelan player to be so honored in Japanese Baseball, joining Roberto Petagine and Alex Cabrera. After playing eight seasons in NPB, Ramirez obtained FA Right in 2008 and was no longer counted as a foreign player for roster purposes. As of 2017, only four foreign players in NPB history had accrued enough service time to achieve the classification. On 6 April 2013, Ramirez hit a home run to record his 2,000 career hit in the NPB, becoming the 42nd player and the first foreign player to accomplish the feat. This accomplishment also earned Ramírez an invitation to the Meikyukai, a private club recognizing Japan's elite players. He was the first Western player to be so honored.
Ramírez spent the 2014 season as a player-coach with the Gunma Diamond Pegasus of Japan's Baseball Challenge League. In 45 games, he hit.305 with 7 home runs and 38 RBI. He retired after the 2014 season and signed on as the Diamond Pegasus' Senior Director.
Coaching
In the middle of the 2015 Ramírez joined the Orix Buffaloes as an advisor, mentoring younger players. In October 2015 he was named as the BayStars manager for the 2016 season, replacing Kiyoshi Nakahata who resigned at the end of the 2015 season due to the team's poor performance. In his first season managing, the team finished 69-71-3, finishing third in the Central League, and advancing to the Climax Series, where the BayStars defeated the Yomiuri Giants, 2-1 in the first round before falling to the Hiroshima Toyo Carp, 4-1, in the league championship round. In his second year as manager, the BayStars reached the 2017 Japan Series, but lost to the Fukuoka SoftBank Hawks, 4-2.
In February 2013, Alex Ramirez started, with his wife and his son, a restaurant in Tokyo, Japan, called Ramichan Cafe, serving the cuisine of Puerto Rico, where his wife grew up. The restaurant has since closed. Ramirez has spoken about his faith saying, "I believe is my desire, but it's not my life. God has already blessed me with this career, and whatever God has planned for me, I will be happy to follow that, whether or not I play baseball again. It's not what I want; it's what God wants for me." As of January 2019, he has naturalised as a Japanese national.