Kaberle was drafted in the eighth round, 204th overall, by the Maple Leafs in the 1996 NHL Entry Draft. Kaberle saw limited playing time in the 1998-99 NHL season. After being eased into the Maple Leafs lineup, he saw a significant increase in playing time in order to help fill in the gap on the Maple Leafs roster after an injury to Bryan Berard in the 1999-2000 NHL season. By the 2001-02 campaign, Kaberle had improved enough to be selected to the World team at the 2002 NHL All-Star game. Later that year, he was named to the Czech national ice hockey team for the 2002 Winter Olympics.
Kaberle started the 2003-04 campaign as a restricted free agent without a contract, and ended up playing in the Czech Extraliga for HC Rabat Kladno while a new contract was negotiated. Ultimately, he signed a contract with the Maple Leafs, securing his services through the 2005-06 season.
On February 11, 2006, Tomáš Kaberle was re-signed to a five-year contract extension worth $21.25 million, with a no-trade clause for the first three years of the contract, effective July 1, 2006. This deal locked him in until the end of the 2010-11 NHL season. On October 28, 2006, he scored his first career hat-trick against the Montreal Canadiens. He also scored in his first shootout attempt that night. Kaberle was named as an Eastern Conference All-Star Game participant for the second time in his career on January 12, 2007.
During a March 2, 2007 game against the New Jersey Devils, Kaberle suffered a concussion, and was carried off the ice on a stretcher, as a result of a late hit to the head by Cam Janssen. While no penalties were called on the play, Janssen was assessed a three-game suspension. In an interview, Kaberle mentioned that Janssen had not contacted him for reconciliation. After missing eight games, he returned to the Maple Leafs lineup on March 23.
Although Kaberle has scored relatively few goals, he has scored seven game-winning goals in overtime.
During the 2008 NHL All Star Game Skills Competition, Kaberle became the fourth player, after Ray Bourque, Mark Messier, and Jeremy Roenick, to hit all four targets in four shots in the accuracy challenge.
Kaberle was selected to the Czech national team in the 2002 Winter Olympics in Salt Lake City, where they were eliminated in the quarterfinals. Kaberle and his brother František were members of the Czech national ice hockey team at the 2005 World Ice Hockey Championships in Vienna, where they won gold. While František won the World Championships for the fifth time, it was the first victory for Tomáš. In December 2005 they were both named for the 2006 Winter Olympics in Turin, Italy, where they won bronze medals with the team. The next year Tomáš accepted his nomination for 2006 World Championships in Riga where the Czech team won silver medals.