Stoner, who had previously tested the RC213V for two days at Jerez in mid-May, confirmed his initial positive impression by leading for most of the day - until Lorenzo, making his 1000cc debut, moved ahead in the final two hours.
Stoner - who extended his MotoGP title lead to 32 over Lorenzo with victory on Sunday - then responded on the 54th of his 57 laps, edging just 0.085sec under Lorenzo's best before rain arrived in the final 30 minutes.
"Today was another good shakedown but we still have some work to do, we found a few positive things and confirmed certain directions to take and move forward," said Stoner, pictured dragging his elbow on the RC213V.
"We had a few small problems with chatter but it's something that shouldn't be too difficult to sort out through engine braking and engine management systems, which are areas we can definitely improve in, along with the chassis.
"The engine for me is fantastic, to ride the 1000 with more grunt and more power it's a lot of fun, it has incredible acceleration, most of the time too much!
"We tested a couple of the new tyres and had some issues, the traction didn't feel that great and they seemed to create a lot more chatter so we went back to the standard tyres and the chatter seemingly disappeared.
"From the data we have from the first test and this test, we can go away and come back with the next step and take it from there."
Unlike Stoner, reigning MotoGP champion Lorenzo didn't race during the previous 990cc MotoGP era (2002-2006), but proved he will have little trouble adapting his style to the larger engine capacity.
Team-mate Ben Spies, looking forward to the 1000cc era after a glittering career on 1-litre Superbikes, also underlined both the potential of the new Yamaha and his own capabilities by lapping just 0.138sec from Stoner.
Unlike Repsol Honda riders Stoner and Dani Pedrosa, who rode only 1000cc machines, Lorenzo and Spies also tested their present 800cc bikes. For that reason, the Yamaha riders only completed around half as many 1000cc laps as Stoner.
Lorenzo was fastest of the 800cc bikes present, finishing fourth overall on the timesheets with a best lap of 1min 56.727sec from 58 laps.
That was just under half-a-second from his 1000cc pace, but 0.9sec quicker than his best race lap on Sunday, when a front-tyre gamble left him in fourth position. Spies - struggling with a pinched nerve in his neck this weekend - concluded testing at lunchtime. He remained the second best 800cc rider, 0.457sec behind Lorenzo.
The overall impression from the Brno test was the 2012 Honda and Yamaha are not only evenly matched, but are also going to be much quicker than even the best of the 800cc bikes - despite having bore/stroke restrictions.
That's not a good sign for Suzuki, whose best hope of remaining in MotoGP seems to be continuing to use this year's 800cc bikes. Suzuki will hope that the equal fuel limit for both 800 and 1000cc entries means the 1-litre bikes have to reign in their pace to last the distance.
Sixth fastest on Monday was the 1000cc Honda of Dani Pedrosa, who crashed out of the lead early in Sunday's race. Pedrosa, a race winner in the 990cc era, was making his RC213V debut after missing the Jerez test due to injury.
The Spaniard rode for 37 laps, the best of which was just over one-second from Stoner.
The factory Ducati team - which has completed five days of private 1000cc testing with its MotoGP riders - stuck exclusively with this year's machines, thus avoiding a direct comparison with the 2012 entries from the two main Japanese factories.
Nicky Hayden was the quickest of the Desmosedicis, the American - seventh on Sunday - finding a significant 0.731sec improvement over his best race lap during his first proper outing on the GP11.1 (after a short debut in practice at Laguna Seca).
That put the 2006 world champion 0.8sec behind Lorenzo's 800cc test time and 0.15sec ahead of MotoGP rookie Cal Crutchlow, who bounced back from another race crash to set a highly promising test pace for Monster Yamaha Tech 3.
Honda LCR's struggling Toni Elias also split the factory Ducatis - with a lap 1.1sec from Lorenzo on the 800 before a big crash ended his test. Next up was Valentino Rossi, who finished 0.733sec behind Hayden after his 74 laps.
Countryman Loris Capirossi was just a tenth slower for Pramac Ducati, with Colin Edwards in turn a tenth further back for Tech 3 Yamaha.
Also on track on Monday was the Marc VDS Suter, a BMW-powered (1000cc) CRT entry being developed for next year.
Former MotoGP and present Marc VDS Moto2 racer Mika Kallio was once again at the controls, the Finn lapping 3.976sec slower than Lorenzo's 1000cc time - a significant improvement compared with the 6.3sec deficit (to the best 800cc bike) at June's Mugello test.
The Suter was a fraction slower than the best WSBK race lap from July's event, but did comfortably beat the best race laps by the BMW S1000RR riders.
Notable absentees were Sunday's podium finishers Andrea Dovizioso (Repsol Honda) and Marco Simoncelli (Gresini Honda). Both are yet to sign for 2012, preventing a 1000cc debut - and they didn't even appear on their 800cc bikes.
Round 12 of the MotoGP World Championship will be held at Indianapolis Motor Speedway on August 28.
