Reports are that a barrage of SA3 and SA5 were fired at the IAF aircraft, and a mobile newer SA17, the newer Buk system, also fired on them. The SA17 is much more dangerous than the older systems, but any of them could have been the missiles that hit the iAF planes. Several defense sites have said an F15 variant was damaged and had to make an emergency landing as well.
There are pics online of a dud AGM130 stuck half way into the pavement on a road, no doubt launched by the IAF - the pics of the F16 crash look like it landed pretty flat, you can make out the front part of the aircraft pretty well which didn't burn much. Both IAF pilots got out, one with serious injuries, and there are pictures of both of them after being picked up by a SAR helicopter online too.
It is eye opening, I agree, as the IAF has typically been able to hit targets in Syria (and elsewhere) at will, and their EW and ECM systems have worked very well recently. There are some pics of Syrian SAM smoke trails flying right at IAF jets (their contrails at least), and then both SAMs trails veer off in formation, the pictures got a lot of press a couple years ago when they went online, obviously showing that IAF EW works pretty well. The shoot down of the F16 and the F15 being hit as well - perhapds the SA17 systems that launched work a bit better than thought, perhaps it was also the number of missiles in the air, reports are saying over 2 dozen were launched in a very short timespan, and that's a lot to defend against at once in such a small piece of airspace.
After the F16i was shot down, the IAF attacked 3 SA5 and SA17 batteries and destroyed them, as well as a bunch of other targets. An IAF Apache also shot down the drone (Iranian Israel has claimed) that entered Israel's airspace as well, video online of that, IAF spokesman said they wanted to shoot it down well inside Israeli airspace in order to get intel on what was left of it (not much by the video, it was blown into small bits from what I could see).
It's the first IAF loss from enemy first since 2006, and that was a helicopter that was shot down IIRC, and not a small tactical one, but a larger transport.
edit - Today (Feb 11th), the IAF has said that the F16i was fired on by 4 different batteries and types, including SA6 units as well as the previously mentioned other 3 systems. They also claim it wasn't a direct hit, but shrapnel from a SAM that detonated close to the F16i, which sounds reasonable based on the pictures of the crash, it looked to be pretty intact when it bellied into the ground.