Editing and emphasis mine, for the sake of clarity.
QUOTE ("SR5 @ p. 192)
Surprised characters are unaware... either because they failed to perceive something... or because the gamemaster decides that they didn’t have a chance to perceive it.
In some circumstances, gamemasters may wish to give a character the chance to be alerted that something is about to happen. The best way to do this is to make a secret Perception Test for the character.
A character who succeeds in the Perception Test is alerted in some way and receives a bonus on his Surprise Test.
The surprise rules below apply to all situations, whether all the parties involved are caught off guard or whether one or more parties are intentionally ambushing others.
To resolve surprise situations, all participants must make a Surprise Test, rolling Reaction + Intuition (3). Characters who have been alerted in some way receive a +3 dice pool modifier on this test. Surprise Tests do not have a Limit.
Success means individuals get to act normally. Failure means characters lose 10 from their Initiative Score (either when Initiative is rolled or immediately if it occurs in the middle of the Combat Turn) and they are considered surprised until their next Action Phase. Surprised characters get no Defense Test when attacked. This can be avoided by spending a point of Edge to avoid surprise. They still lose the Initiative Score points, but they can at least use their defense rolls.
So let's run through a quick example.
Ninja Runner is Sneaking along, when he turns a corner and almost bumps into Corporate Guard. The Guard isn't Sneaking, and is in normal clothing in normal lighting and visibility conditions, so the GM rules that Ninja doesn't even have to roll perception and automatically detects him.
However, Guard doesn't succeed in his Perception check to notice Ninja - who is wearing a Chameleon Suit and actively Sneaking - so Guard is automatically unaware. The only thing being "unaware" means is that Guard doesn't get the +3 on his Surprise Test.
Both Ninja and Guard roll their Reaction + Intuition. In this case, Ninja gets a solid 5 hits, so the Guard has not surprised Ninja. However, poor Guard only got 1 hit, so Ninja has surprised Guard. Combat begins, Initiative is rolled, and Guard suffers -10 Initiative. He rolled an 8, so that gets reduced to -2, meaning Guard doesn't get to act this Combat Turn. He also is Surprised, meaning he can't take any defensive actions. Ninja swings his sword and Guard just eats it - Ninja gets 5 hits on his attack, which all count as net hits for extra damage. Ouch! Unfortunately for Guard, Ninja rolled a 19 on his Initiative, so here comes another swing! I can't watch!
Let's back up for a second, though. Let's say that instead of rolling an 8 on Initiative, Guard instead rolled an 11. His penalty for failing his Surprised Test drops him 10 Initiative, and he still can't defend, but he's left with exactly 1 Initiative, meaning this time he gets to take an action before Ninja can use his second Initiative Pass to finish him off. Guard can't use his action to fight back - characters who are surprised cannot act against nonsurprised ones - but he's going to spend his turn calling for backup and running as far away as he can from the sword wielding psycho. Good call, Guard!
Let's go another step back. Let's say that Guard and Ninja are in a creaky old building with wooden floorboards, and that the GM decided this gave Guard an extra Perception Test to be able to detect Ninja's approach. This time around, Guard gets lucky and manages to hear Ninja coming! He's no longer "unaware", and he gets a +3 bonus to his Surprise Test. Those +3 dice really help this time - instead of only 1 hit, Guard manages to squeeze out 3 hits, meeting the Surprise Threshold! He manages to react quickly enough to the sound of creaking floorboards to not be taken by surprise! At this point, combat occurs as normal, because neither Ninja nor Guard are surprised.
Let's go one final step back. Let's say that instead of sneaking around a corner and accidentally bumping into Guard, Ninja is lying in wait ready to Ambush whoever comes around the corner. The ambushing rules (which I did not quote above) tell us that an Ambusher receives +6 on their surprise test, and that they are immune to being surprised by their prey, assuming they can actually see them coming, or otherwise are aware of their movements. So when Guard comes around that corner, Ninja will almost certainly not be surprised by him!
Except that Guard doesn't come around the corner. Ninja waits a little but all is quiet - too quiet. He begins to sweat, and he gets a creeping feeling down the back of his neck. Suddenly, something big, hulking, metallic, and possibly even once-human is behind Ninja, looming over him! He failed his Perception Test to spot the chameleon coated cyberzombie creeping up from behind! Oh drek! Fortunately, Ninja was primed for an ambush - he gets +6 on his Surprise Test, and easily clears the threshold of 3 to avoid being surprised. That said, it's a darn good thing he did beat the threshold, because being caught surprised and unable to defend or act against a cyberzombie is bad news! Meanwhile, the cyberzombie is immune to being surprised by Ninja in this test, because the cyberzombie crept up and
ambushed Ninja!
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TL:DR - Yes, if he can see his prey while ambushing, they cannot surprise him. Also, I agree that the flat (3) Threshold doesn't feel right - in SR4 you compared test results between characters, and anyone with a lower total than you was surprised by you. Even your allies!
~Umi