A first-half goal by Tunji Akinola and a stoppage-time second from fellow centre-half Kevin Holt put the visitors through to a last 16 tie with Queen of the South.
But despite seeing his side exit from the competition, the Blues boss was looking on the bright side as attention turns back to League 2 and this Saturday’s home match with Edinburgh City.
“They [Partick Thistle] are a good Championship team and will be there or thereabouts at the end of the season,” he said.
"Ian McCall's got the boys playing really well, so it was a good test for us yet again.
"To lose a late goal and come away 2-0 was disappointing considering the second half we had. We created three or four good chances but it just wasn't to be.
"We're not too disheartened, we just keep plodding on and working away."
"In the first half we got into a wee bit of a battle where the ball was going forward tit for tat.
"I was looking for the boys to have a wee bit of composure, put their foot on the ball.
"They're a tough Championship team but I thought we equipped ourselves [well] and the second half was a wee bit more pleasing.
"On the whole it's never nice to come away with a 2-0 defeat, especially on the back of a good win on Tuesday night, but the boys have just got to dust themselves down and look forward to the league game on Saturday.
"I don't really think we tested the goalkeeper too much, but we're still creating chances which is pleasing. We just need to keep working hard and I'm sure we'll be OK.”
Hamill hasn’t had his problems to seek in terms of players being out recent, particularly goalkeepers.
With Curtis Lyle, on loan from Kilmarnock, missing with a shoulder injury Luke Scullion came in against Thistle for only his second match and made some fine saves against his old club.
Hamill said: “His handling and his kicking were excellent today, he's a good goalkeeper and has made a claim for the number one jersey with Curtis being out.
"We just need to get to the bottom of how long Curtis is going to be out because we're still unclear.”