The Mercedes driver had headed the morning running, but improved his time in the afternoon using the Pirelli C5 tyres, which are two steps softer than the softs used during the grand prix but will be available in Monaco next weekend.
He set a time of 1m15.511s, just 0.105s slower than his record pole position pace from Saturday.
At the same time, Toro Rosso driver Daniil Kvyat moved up to third, setting a time of 1m17.679s.
Renault driver Nico Hulkenberg secured fourth place half an hour after running resumed with a time of 1m18.051s set on the C3 Pirellis.
Red Bull driver Pierre Gasly had an early end to his programme when he ground to a halt with 70 minutes remaining with a suspected transmission problem that struck at the exit of the chicane.
By that time, he had completed almost 115 laps – having ground to a halt a few metres before the line – and done enough for fifth place, 2.629s off the pace with his time set on C3s.
HAAS tester Pietro Fittipaldi jumped up to seventh place in the closing minutes with a time just 0.063s slower than Sainz, putting him just 0.035s ahead of Racing Point simulator driver Nick Yelloly.
Sebastian Vettel’s Ferrari, one of two cars conducting tyre testing for Pirelli, was ninth fastest on unmarked rubber.
Sergio Perez also didn’t improve in the afternoon in the Pirelli test Racing point, ending the day a tenth faster than Alfa Romeo’s Callum Ilott.
Ilott’s day came to an end just before the halfway point of the four-hour afternoon session when he crashed heavily at the fast Turn 3 right-hander the lap after he had set his best time.
He escaped injury but the car was too badly damaged to get back out again before the end of the session.
Full results to follow