Born in Etya, Arsi Province, Gezahegne's first international competition was the 1999 Los Angeles Marathon, where he finished fourth, behind three Kenyans. That earned him a place in the Ethiopian 1999 World Championships team, where he finished eleventh.
Later in the 1999 season, Gezahegne won his first international marathon by finishing first at Fukuoka marathon in Japan. He won this marathon again in 2001 and 2002. In 2000, Gezahegne finished second in the Boston Marathon.
At the Sydney Olympics, the marathon race came down to two Ethiopians, Gezahegne and Tesfaye Tola, and Kenyan Erick Wainaina. At the 37 km mark, Wainaina tried to make a break, but 2 km later Gezahegne surged to the lead and held the position to the finishing lane. At 22 years old, Gezahegne was the youngest marathon champion since Juan Carlos Zabala in Los Angeles 1932.
In 2003, Abera won the London Marathon in 2:07:56. At the 2003 World Championships, Gezahegne had to abandon the race due to injury, but he was selected in the Ethiopian 2004 Olympic team. Again. injury kept him from the race. His wife Elfenesh Alemu was also selected to the 2004 Olympic team, finishing fourth in the women's marathon.
Gezahegne's repeated injuries ended his running career at a relatively young age. He and his wife own a hotel and property development business.