Late replacement Watt was forced to step into the breach after Jason Doyle, himself deputising for crocked Pirates star Darcy Ward, withdrew following a crash in his first race against Latvia in Landshut, Germany.
Former world champion Holder, who made a swift return to Elite League action after fellow countryman Ward had sustained a knee injury in the Grand Prix series opener in Auckland last month, won three of his six heats and racked up 18 points before taking a fourth chequered flag in the final.
Having won his first heat, Watt, who rides in the Elite League for Lakeside, went on to score 17 before falling on the first turn of the final against Denmark.
In the re-run, Holder led throughout while Watt recovered from a poor start to pass Nicki Pedersen and Niels-Kristian Iversen but was pegged back by the latter during lap three.
The Danes qualified for the showdown with the Aussies having beaten Poland in the semi-final.
Pirates’ Polish star Shamek Pawlicki, called up after GP series leader Krzysztof Kasprzak had crashed and withdrawn, finished last in all three of his heats.
Australia’s victory kept them at the summit, four points clear of Denmark with two out of three meetings completed.
The final leg of the European Best Pairs series takes place on Friday, May 23 in Eskilstuna, Sweden.
Meanwhile, Holder and Watt will be in opposition when Pirates host the Hammers in the Elite League at Wimborne Road on Wednesday. Third-placed Pirates are currently four points behind table-topping Lakeside.
European Best Pairs standings: 1 Australia 20pts, 2 Denmark 16, 3 Poland 12, 4 Sweden 7, 5 Germany 4, 6 Russia 3, 7 Latvia 3.