After the visitors had equalised Shola Ameobi's disputed first half opener just after half-time - Defoe having played a key part in the build up - the Hammers striker put England ahead for the second time when he struck in the 67th minute, just a few minutes after having what looked a good goal ruled out for offside.
But this time Defoe timed his run to perfection, receiving a clever through-ball from Jermaine Pennant before rounding the keeper and rolling the ball into the unguarded net from 12 yards - his seventh goal in 18 under-21 internationals.
By then, he had been joined on the field by his two Upton Park team-mates. Goalkeeper Bywater was called into action within minutes of the start of the second half after Rhys Evans suffered a back muscle injury in his vain effort to keep out Serbie & Montenegro's spectacular first goal.
Although Bywater didn't make a save, he saw plenty of action. The ball twice luckily rebounded from the England bar and post before Stanic drove home the visitors' second equaliser from 20 yards five minutes from full time, with the young Hammers keeper possibly slightly unsighted.
Johnson, who replaced Stuart Parnaby on 57 minutes, made some typically positive, thrusting runs down the right flank to again impress manager David Platt.
England's winner, their first in four matches, came from Darren Bent of Ipswich Town in the 87th minute.
All three Hammers could start when England resume their European Under-21 Championship group qualifiers against Slovakia at Sunderland next Tuesday (June 10).