Molloy was a late withdrawal from their St Kilda clash with what was initially described by the club as "knee soreness" before club officials confirmed she had ruptured her anterior cruciate ligament.
The 25-year-old learnt her season was over just hours before the Saints match after hurting her right knee during training earlier in the week.
Molloy hid the information from her teammates until after their eventual 16-point loss.
"Chloe herself came up and said she just didn't want to tell the players, which I was really comfortable with, and didn't need the distraction," Gowans said on Tuesday.
"It was such a quick process from finding it out and then having it confirmed.
"I was a little bit interested by some of the commentary around it to be honest, but I think we followed the process that we needed to follow and just made the late change."
Gowans admits the shock and devastation around Molloy's injury has yet to sink in, given the three-time All-Australian was able to continue training after injuring her knee.
"This is typical Chloe. She went off for maybe two or three minutes and came back on the ground," he said.
"We're doing a full ground ball movement drill, went into the pocket. Chloe's picked the ball up cleanly, twisted around and kicked the ball through the goals on her right foot.
"I thought 'She's right', didn't think anything of it, and then went to bed fully expecting she was playing.
"Even at the hotel, (she was) walking around. She was typically annoying Chloe, just annoying.
"She was fine. It was just no signs of anything sinister.
"And then from there, we found out the next morning, the doc confirmed it with me and just said, 'I hate to tell you this'."
Gowans added Molloy will continue to have a match-day role in the coaches' box or on the bench.
The Swans will be hoping to get back to their winning ways when they host the Tigers at C.ex Coffs International Stadium in Coffs Harbour on Saturday.
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