During spring training in 2008, on March 12, Gomes rushed to the defense of Akinori Iwamura when the latter was spiked by Shelley Duncan of the New York Yankees. Gomes immediately rushed in from right field, flinging himself into Duncan as he was beginning to stand up. This emptied both teams' benches, as players and coaches ran onto the field. Gomes and Duncan were both ejected, as were two Yankees coaches. Due to his actions, he was suspended for two games, effective at the start of the season. Gomes commented that his actions were simply coming to the defense of his teammate, saying "I was taught in T-ball all the way up, to always protect a teammate's back. I just acted how I act. I wasn't really trying to get a shot in on him. I probably could have done a lot of things worse. But it is a baseball field and there's fans and kids watching. I just had to let him know that's not going to fly."
In the third game of a series against the Boston Red Sox on June 5, 2008, Gomes was involved in a bench clearing brawl after Coco Crisp charged the mound as a result of, among other events, being hit by a pitch. Replays of the incident show Gomes throwing punches at Crisp as he was already being shoved to the ground by several other Rays players. He was suspended for five games due to his role in the brawl. On August 6, Gomes was optioned to the Durham Bulls of the International League to create roster space for Ben Zobrist, and he was recalled after rosters expanded in September. The Rays would play the Philadelphia Phillies in the 2008 World Series but would lose in 5 games, Gomes did not play in the World Series. Gomes was the only Rays batter to hit a homer while serving as a pinch hitter in 2008.