"I've been through so much hard work to reach this gold, I've had so much support but also so much pain, but in the end it all paid off," he said after beating Lee Dae-hoon of South Korea in the final.
"We've never managed to get gold in taekwondo until now so I'm so glad and it's so great to be the first one.
"It's been a fantastic year for me, I won the 2011 world championships and now the Olympics. It's the icing on the cake after four years of hard work."
Bonilla swept through the competition and was particularly impressive in the semi-finals where he demolished Oscar Munoz Oviedo 13-4.
He faced his toughest opponent in the final but was quicker and more accurate with his kicks than the shaggy-haired Korean, jumping into a 5-2 lead in the first round.
Lee came back strongly but the Spaniard seemed to easily anticipate his opponent's attacks and made him pay in the second round, picking him off as he rushed in.
Midway through the round Bonilla decked Lee with a straight kick to the Korean's face, bringing the crowd to its feet and moving the Spaniard into a seven-point lead.
Lee threw caution to the wind in the final round and put Bonilla under immense pressure but he never looked flustered and continued to pick the Korean off to win 17-8.
The silver medallist, who had dropped down to 58kg from the 63kg category to compete at the Olympics, which only features four weight classes, was disappointed to miss out on gold but had no regrets about the final.
"He's very tactical and I had a great match with him and so all in all I'm still happy with my silver," said Lee. "It could have been better with the gold but silver medal is something great."
Colombian Oviedo and Russian Alexey Denisenko won the bronze medals through the repechage competition.