The 20-year-old 2011 world champion followed Maria Isabel Urrutia to Olympic glory, 12 years after the weightlifter won in Sydney.
Maris Strombergs triumphed in the men's race for Latvia's first gold of London 2012.
Pajon said: 'I'm very happy and proud. This is a very strong moment for Colombia cycling, there's been a lot of support in recent years and that's beginning to give results.
'It was a great moment for Colombia. Back then (in 2000) I was a gymnast and didn't do BMX.
'I thought I would come to the Olympics as a gymnast. I saw those moments and they fill me with pride and I wanted to come to the Olympics.'
I'm very happy and proud. This is a very strong moment for Colombia cycling, there's been a lot of support in recent years and that's beginning to give results.Mariana Pajon
Strombergs won one quarter-final run and finished third in semi-final heat two to advance to the final, where he showed his quality.
The 25-year-old found his top form at the right time to successfully defend his title ahead of world champion Sam Willoughby of Australia and Carlos Oquendo of Colombia, who were second and third respectively.
Strombergs said: 'It's just an amazing feeling. I think everybody at home, they watched the race and deep inside they, not expected it, but they were hoping that I could repeat. I think the whole country believed in me.
'This one means a lot more to me. When you grow older you start to appreciate things more. So this one is more special.
'For myself, it just gets tougher against these young kids. I can see myself out there. I'm one of the old guys in BMX and I'm just 25. When you get older you start thinking more.
'Deep down I was still confident and I'm happy that I was able to put together one good race.'