Humphreys ended his 22-year association with the province when he left the RaboDirect PRO12 side on Saturday to take up a similar role with Gloucester.
And Best, who is currently on tour with Ireland in Argentina, paid tribute to his former boss.
"He's not just been a part of Ulster rugby, he has been Ulster rugby," Best told the Irish Times.
"I was very surprised. Obviously he's had a big association with Ulster rugby, not just for the last few years as director of rugby but since the late 1990s.
"So, obviously it is a big shock but I suppose he has to do what's right for him and his family, to experience something new.
"It's no different from us as players, when opportunities like this come along. You want to finish with no regrets, it's just something he had to do.
"Obviously, it's bitterly disappointing but you have got to wish him all the best like you do with every player that leaves."
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