A late fast lap by MotoGP title leader Jorge Lorenzo put the Factory Yamaha star on top of the Aragon test timesheets by 0.255s over team-mate Ben Spies.
Spies had been fastest for most of the day, at a test notable for the absence of Repsol Honda riders Casey Stoner and Dani Pedrosa.
HRC chose not to make the journey from Catalunya, where Monday's post-race test was held, since the new specification Bridgestone front tyre - which Stoner and Pedrosa are currently struggling to find a set-up for - was not made available at Aragon.
Some of the CRTs were also absent, but 14 of the 21 full-time riders took the opportunity to test at a venue which will host round 14 of this year's world championship in late September.
The main task for Lorenzo and Spies was to further evaluate a new engine and electronics package, whilst also working on finding a 1000cc set-up for the Spanish track.
Lorenzo rode for 59 laps (his best being the 57th) while Spies - who has suffered a nightmare start to the season - gave his confidence a further boost during a similar 57 laps (best 55th).
Following the factory M1 riders on the timesheets was the satellite Tech 3 Yamaha pairing of Crutchlow - half a second behind Lorenzo - and Andrea Dovizioso, a further two tenths down.
Dovizioso, fastest in Monday's Catalunya test, continued his work on electronics, engine, and track set-up, while Crutchlow made up for lost time after suffering a heavy fall early in the Catalunya test.
Pramac Racing Team's Hector Barbera was fastest Ducati once again in fifth (+1.009s) as he evaluated electronics, while Nicky Hayden was a few thousandths slower to be the top factory Desmosedici rider in sixth.