Bowe, 30, scored the second of Ireland's tries in Saturday's 29-15 win over South Africa at the Aviva Stadium.
He has won 55 caps for Ireland, scoring 27 tries, and has made 124 appearances for Ulster, scoring 48 tries.
Earlier this week, the IRFU confirmed that Rob Kearney had also signed a new three-year deal to stay with Leinster.
Bowe made his competitive debut for Ulster against Connacht in April 2004 and enjoyed a spell with the Ospreys, before returning to his home province for the 2012-13 season.
He made his Ireland debut against the USA in November 2004 and has twice toured with the British and Irish Lions.
The Monaghan man played in all three Lions Tests against South Africa in 2009, and in two Tests in Australia in 2013.
He was a member of Ireland's 2009 Grand Slam-winning team and was named Six Nations Player of the Championship in 2010.
"I'm delighted to have signed a new contract with the IRFU and Ulster," Bowe said.
"It is an exciting time for both the province and the national team and I hope to play a part in achieving success on both fronts in the years to come."
Ireland winger Tommy Bowe will remain with Ulster until at least June 2018 after signing a new three-year contract with the IRFU.