Pakistan thumped England by 72 runs in the second Test here on Saturday, taking an unassailable 2-0 lead in the three-match series. They won the first Test by ten wickets in Dubai. The third and final Test begins in Dubai from February 3.
Under Flower England had been unbeaten in their last nine Test series, which saw them rise to number one in rankings last year. But after being set a tricky 145-run target to win on Saturday, England were dismissed for a paltry 72 runs as Pakistan's spin bowlers came to the fore.
"We realise that we haven't been very skillful in dealing with that type of cricket. In saying that, it's also right to praise the Pakistan team for what they have done. They beat us fair and square," said Flower.
"They have beaten us properly in two matches. They have fought hard and worked hard at their game and in a way I'm very happy for them. It's good for their cricket and it's good for their country."
Flower, a former Zimbabwean batsman, said defeats were a 'wake-up' call for England. "It was a wake-up call no one wanted to get. Not to that degree. But, yes it is," said Flower.
"Yesterday (Saturday) was very poor. The three days preceding that were pretty good. We put ourselves in a good position where we could have won the Test but then performed very badly with the bat to lose it.
"We didn't put any pressure on their bowlers in the second innings. We allowed them to bowl and create pressure. In saying that, the conditions to play against quality spinners were difficult and we weren't good enough."
Pakistan spin duo Abdul Rehman, who recorded career-best figures of 6-25, and Saeed Ajmal (3-22) led the fightback after they had conceded a first-innings lead of 70 runs. Flower said dropping a few catches in the first innings was crucial.
"Maybe we dropped a couple of important catches, but other than that the bowlers and fielders were outstanding and Monty Panesar was great. But obviously our batting against spin let us down."
England dropped Misbah-ul Haq on 30, who went on to make 84. Panesar, playing his first Test since the Cardiff Test in 2009 Ashes, took 6-62 to bowl Pakistan out for 214 in the second innings. Flower admitted that not playing well in the subcontinent was a big challenge to overcome.
"This is a great challenge for all of us. The issues are not going to disappear. We've got another Test. We've got a one-day and T20 series, and then we've also got Sri Lanka and India before the year is out.
"So these issues will not disappear and we've got to face them with skill and a bit of courage. We've got to be a lot better than we were yesterday. Each individual will have to work very hard in working out his method of scoring."
When asked if batsmen repeating mistakes was frustrating, Flower said: "I think that is fair comment, yes. We expect to learn quickly and that is a big part of our job, and my job."