I've seen some conflicting information on the web about yellow fever vaccinations at the El Dorado airport. I just got a vaccination today (Aug. 2017). There is the Fontibon Hospital on the Second Floor (Departures Level) tucked in the back of the terminal (I had to ask the people at the Information Desk where it was, as it's not listed on the map).
There's a small lobby where people wait. You register at a computer where you pick up a number, which essentially puts you in line. You need some form of identification (e.g., passport) and you need to sign some forms. I have 0 Spanish and I managed to get through just fine, but some basic Spanish definitely won't hurt. In all, I had to wait for 7 people ahead of me and the whole process took about 30 minutes (including the waiting).
I'm currently living in Bogotá, though, so I have some time before taking trips into the jungle (Macarena, Leticia, etc.). Having just set up a trip to Macarena with a travel agency, my understanding is that you cannot board planes at El Dorado that are headed to 'at-risk' areas without the documentation that says you got vaccinated. Maybe the travel agency just wanted to scare me into getting the vaccine, but I wasn't going to roll the dice. In any case, it seems like the Colombian government has doubled down on making sure that everyone has yellow fever vaccinations before traveling to areas where people might contract yellow fever.