Australia were comfortably beaten by 221 runs in the first of two encounters in the longer format, having achieved a clean sweep in the earlier Twenty20 and one-day matches.
And Gilchrist reckons the team's Test woes in Dubai were down to psychological reasons, rather than a lack of quality.
"It was more of a mental issue than a skill issue," he told Sport360. "They found adapting to the conditions a little more difficult than what they expected.
"Michael Clarke came into the team with not a lot of cricket under his belt. These are conditions that take a lot of time to adjust to.
"If you look at Pakistan, they played some good old-fashioned patient Test cricket, which is becoming more and more rare.
"In the end, it was about our batsmen not slowing down their natural game to suit the tempo of what was in front of them."
Gilchrist, who played 96 Tests during his career, also feels it was difficult to predict how Australia would perform in the first Test, despite their success in the shorter formats.
"It's so difficult in this day and age to have long tours with two or three tour matches," he added. "The onus is on the players to get themselves right mentally and physically.
"They did have success in the T20s and ODIs, but they had at least four or five personnel changes so it’s difficult to take into account any success in those formats."
The second Test begins in Abu Dhabi on Thursday.