After victories over Faroe Islands minnows NSI Runavik and Northern Ireland part-timers Crusaders, the west Londoners endured a frustrating night at Dugopolje's Stadion Hrvatski Vitezovi in Croatia as they struggled to a goalless draw in the Europa League third qualifying round clash.
Split proved dogged opponents throughout and were unfortunate not to score on several occasions, with Ante Erceg and Duje Cop both missing gilt-edged chances.
Hughes was quick to praise Split for the manner of their performance, but insisted the Cottagers did not take their opponents lightly.
"We kept a clean sheet, which is one of the positives we take from the game," he said.
"We expected a tough game from them and that is really our first real test of the competition.
"The other games were difficult for maybe different reasons but we knew coming out here, regardless of who we played, they were going to be of a decent standard.
"Physically they're in decent shape, technically they were good and the standard they play at whether it be club level or international football.
"So we knew we were in for a more difficult game and to be fair to them they played well. They kept the ball well at times and we were solid enough.
"We maybe had one or two moments when we had a little bit of a scare but apart from that I think we were pretty solid.
"But, like I said, we are happy to get the clean sheet and take them back to Cottage and have a real try to win that and go to the next round."
When asked whether they surprised Fulham with their quality, he said: "No, not at all. I don't know how they were perceived outside [the dressing room] but certainly we watched a bit of them on DVD and they were what we thought they would be.
"Like I said, they were well organised, they would be physically strong, technically good and they played well.
"They rose to the occasion, they didn't hide and they were confident on the ball.
"So there were no surprises on our part, it was totally expected, which is why we are happy to come away with a clean sheet and still have plenty to play for."
Fulham named recent signings Marcel Gecov and Pajtim Kasami on the bench for the first time last night, with the latter coming on for his Fulham debut 10 minutes from time.
"They are very good, very good," said Hughes.
"We've obviously not seen much of them (against Split), but in training and that they have looked very good, very accomplished, tidy players that are technically good and good on the ball.
"And to be fair to them they have come in and settled in really well, which I don't think is a hard thing at Fulham because the lads here are pretty welcoming.
"They get everyone in straight away and make them feel at home so no, they've looked really good."