"We needed the break as well, and you cannot have it all ways," Flower added.
"The players needed the mental and physical break from the rigours of competition.
"But we weren't on the ball and weren't sharp enough to deal with what Pakistan challenged us with in this game."
England, the world's number one Test side, were bowled out for 192 and 160 in what was their first Test in the United Arab Emirates.
Test Match Special Analysis
Michael VaughanFormer England captain & TMS pundit
England have started the series so badly it now comes down to the mentality of an individual player. Can the individuals adapt, look at the videos - can they pick Saeed Ajmal? There are only one or two of the guys who are picking him. Jonathan Trott did, and Matt Prior did in the first innings. But the rest of them weren't picking him, and that's a real concern. Ian Bell got a good delivery in the first innings, then he was out again to the same ball in the second innings
Off-spinner Saeed Ajmal took 7-55 in the first innings, while pace bowler Umar Gul dismissed Andrew Strauss, Alastair Cook, Jonathan Trott and Kevin Pietersen in the second as England's top six mustered only 143 runs between them in the game.
"We didn't play him well," Flower said of England's failings against Ajmal.
"As a batting side, a number of our individual batsmen made poor decisions, and this result is a sum of those decisions.
"Tomorrow, we have access to the spin bowling machine 'Merlyn', and it is a chance for our batsmen to get clarity about their game plans against spin.
"We have been exposed in this Test match, and need to come back better in the next one."
Flower has warned his players they must improve markedly when the second Test gets under way on 25 January in Abu Dhabi.
"You have to play really well in Test cricket to beat the opposition," he said.
"They outplayed us by a long margin in this Test and deserved the victory.
"It is now our challenge to get back on track, and put them under some pressure at the start of the second Test."
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