Gonzaga upset Filipovic at UFC 70 in Manchester, England, leaving the Croatian sprawled on the canvas after absorbing a head kick in the first round.
The 40-year-old Filipovic went 7-1 in kickboxing and 3-1 in MMA since his last fight in the UFC, a loss to Roy (Big Country) Nelson in October 2011.
Gonzaga was the early aggressor Saturday in the UFC's first-ever card in Poland and took Filipovic down midway through the first round. Gonzaga, a black belt in Brazilian jiu-jitsu, mounted Filipovic only to have to fight off an attempted heel-hook.
Filipovic (31-11-2 with one no contest) looked for a head kick of his own in the second round but went down again after Gonzaga grabbed a leg. Filipovic was mounted again and took some damage, with an elbow carving him open by the left eye.
The tide turned in the third when Filipovic hurt Gonzaga with a pair of standing elbows. Gonzaga went to the ground and Filipovic finished him off with more elbows at 3:30 of the round.
The 35-year-old Gonzaga (16-10) is ranked 14th among heavyweight contenders.
Filipovic was considered an iconic heavyweight when he joined the UFC in early 2007 after winning Pride's open weight championship in Japan. A devastating striker, the former K1 fighter was once famously quoted as saying "right kick hospital, left kick cemetery.''
But he could not reproduce that deadly form in the cage posting a 4-6 UFC record prior to Saturday.
In the co-main event at the Tauron Arena, London-based American Jimi (Poster Boy) Manuwa won a 30-27, 30-27, 29-28 decision over Polish light-heavyweight Jan Blachowicz (18-4).
Manuwa (15-1) said he fought despite suffering an injury in the leadup to the bout.
Ranked ninth among 205-pound contenders, Manuwa was beaten by No. 1 Alexander (The Mauler) Gustafsson of Sweden last time out.
Earlier on the main card, Canadian Sheldon Westcott lost a unanimous decision to Polish welterweight Pawel Pawlak.
All three judges scored it 29-28 for Pawlak (11-1). The loss was the second straight for Westcott (9-3-1).
"I didn't fight very well, it was tough. It was so tough," Westcott said afterwards. "But the crowd was awesome out there."
Westcott started aggressively and came at Pawlak, tying him up at the fence for most of the round. It went that way most of the fight with Pawlak resisting Westcott's attempts to get him to the ground.
Pawlak had more success taking Westcott down, using trips from the clinch.
Pawlak, a gardener when not fighting, hurt the 30-year-old from St. Albert, Alta., with a pair of knees early in the second round, driving him to the ground. But Westcott recovered and continued the fight at the fence.
It was Westcott's first fight since losing to Elias (The Spartan) Theodorou by second-round TKO in the final of "The Ultimate Fighter Nations" last April.
Earlier, welterweight Leon (Rocky) Edwards needed just eight seconds to knock out Seth (Polish Pistola) Baczynski.
The UFC says Chris Camozzi, stepping in for the injured Yoel Romero, will face Ronaldo (Jacare) Souza, ranked No. 1 among middleweight contenders, on next Saturday's televised card in Newark, N.J.