Opener Khawaja batted for eight hours and 44 minutes to help foil Pakistan's victory bid, while Travis Head (72) and Paine, who finished unbeaten on 61, played key supporting roles to take Australia to 362-8 and save the match.
Paine and number ten batsman Nathan Lyon (five not out) batted out the final 12.1 overs to snatch a draw, as Australia ended 100 short of a daunting 462-run target set by Pakistan.
"I am just really proud of the whole group, how they stuck to our plans and kept digging in. I am really proud of Usman, too, on one of the great Test innings," said Paine.
"No, it doesn't feel like a win. We were outplayed. Proud to get something out of it, but we can play a lot better in the next Test," said Paine, with the second and final Test starting in Abu Dhabi on Tuesday.
Khawaja, whose best score was 26 in five previous Tests in Asia, admitted it was one of the best innings of his career.
"I normally never sweat through my shirt, but my shirt was drenched and my pants were drenched. That took it out of me a fair bit. I've never had an innings like that," he said.
"To bat that long a period in Asia – it is a bit different. It shows a lot of guts and courage to do something like that," added Khawaja, whose 524-minute knock was the second longest in a fourth innings in Test history.
'Worked My Backside Off'
Former England opening batsman Michael Atherton holds the record after his match-saving 185 not out against South Africa in Johannesburg in 1995 spanned 645 minutes.
Khawaja, who was born in Pakistan but emigrated to Australia in his childhood, said he was proud to have scored a hundred for his adopted country.
"It was mostly about getting a hundred for Australia on the last day of a match, trying to save a game. A lot of work goes into playing cricket at the highest level," he said.
"I work as hard as anyone. I have worked my backside off for the past 10 years, day in, day out."
Pakistan captain Sarfraz Ahmed was also full of praise for Khawaja.
"I think I have seen one of the best innings in Test cricket, especially in the fourth innings. The way he batted he took Australia to a draw and played all his shots," said Sarfraz.
Leg-spinner Yasir Shah, who took only four wickets in the match, was defended by his skipper after Pakistan failed to close out victory.
"He (Yasir) had played the first Test after a year so you have to give him some margin (for error). He is our match-winner so, hopefully, he will bowl better in the next game," said Sarfraz of Yasir, who went wicketless in the first innings.
"Look when we came today we were confident to win the Test, they fought hard and saved it and that's the beauty of Test cricket."
Australia cricket teamPakistan cricket teampakistan vs australia 2018Sarfraz AhmedTim PaineUsman Khawaja
First Published: October 11, 2018, 10:58 PM IST