Sri Lanka were 32 without loss, needing a further 330 runs to reach their victory target of 362, with England 2-0 up in the three-match series.
Dimuth Karunaratne was 19 not out and Kaushal Silva 12 not out.
As Sri Lanka players surveyed the scene, there was no sign of the national flag that had been draped across their dressing room balcony on Sunday in protest at a wrongly called no-ball that denied them a key wicket.
But Australian umpire Rod Tucker had already called a no-ball.
Replays indicated part of Pradeep's front foot had landed just behind the crease but fielding teams are unable to challenge a no-ball call by an umpire and Hales survived.
Under International Cricket Council regulations, incorrect no-ball calls cannot be revoked but umpires can check for a no-ball retrospectively following the fall of a wicket.
The Sri Lanka flag was draped over the tourists' dressing-room balcony for some 45 minutes in protest at Tucker's decision.
"You feel a little down, it is sad," Sri Lanka Cricket president Thilinga Sumathipala told reporters.
"The management on tour is very sad about that decision. It will be reported to the ICC."
Several close Decision Review System calls went against Sri Lanka on Sunday and Sumathipala said: "If the decisions are continually happening against you many times then they (the players) will get demoralised. If they feel it's only happening to us, that's sad."
But with a whole session lost, the chances of either Sri Lanks scoring the runs they needed, or England taking 10 wickets, to force a victory were receding, with a draw now the most likely result.
The umpires brought lunch forward to 12:30 pm (1130 GMT) in the hope of making a prompt start to the afternoon session.
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