The Mauritian Super League side were eliminated from the continental competition after losing to the Buccaneers 3-1 on aggregate in their First qualifying round clash.
They held the Betway Premiership champions to a goalless draw at home before suffering a defeat in the second leg.
Reflecting on their Champions League exit, Thomas praised his players while acknowledging the gulf between his side and Pirates.
"I want to thank the organisation for the welcome, they put us in good conditions to play this match today, congrats to Pirates for their qualification, they showed they are a big club and stronger than us," he said on iDiski Times.
"I am proud of players, they gave everything on the pitch, we are amateurs, La Cure Waves and Pirates is a big club, good players who deserve qualification."
“The match as you saw, it was very difficult, you saw that difference between the players, they are levels above,” Thomas added.
“I wish Pirates advance to the next stage and why not win the African Champions League.”
Milford head coach Xanti Pupuma says his side's first game of their debut season against title-holders Orlando Pirates gave them the confidence they needed to compete in the Betway Premiership.
Orlando Pirates coach Abdeslam Ouaddou has warned his players that individual showboating will not be tolerated if they are serious about challenging for the CAF Champions League title.
Orlando Pirates head coach Abdeslam Ouaddou has admitted the club could be forced to consider its options in the transfer market after being left with just one recognised right-back.
Power Dynamos coach Oswald Mutapa was left reeling after his side were eliminated from the CAF Champions League without scoring a goal.
