The Mali international striker headed home Fahid Ben Khalfallah's 29th-minute cross and then slid a 72nd-minute shot through keeper Rob Elliot's legs to condemn the Magpies to a first European defeat of the season and avenge for their 3-0 defeat at St James' Park in October.
But for Elliot, who made important first-half saves from Henri Saivet, Ben Khalfallah - who passed up a glorious opportunity at the death - and former Sunderland striker David Bellion, they could have won even more handsomely at the Stade Chaban-Delmas.
Newcastle, whose arrival in France on Wednesday night was delayed by almost four hours because of snow on Tyneside, needed a victory to snatch top spot back from Bordeaux, but they rarely looked like securing it as few of the youngsters handed a chance to shine managed to do so.
Only Mike Williamson and Sylvain Marveaux survived from the Magpies' 3-0 Barclays Premier League victory over Wigan on Monday evening, and that meant starts for James Tavernier, Shane Ferguson, Gael Bigirimana, Mehdi Abeid, Sammy Ameobi and, for the first time since April 2010, striker Nile Ranger.
Elliot was called upon for the first time with less than two minutes gone when midfielder Saivet was allowed to control skipper Gregory Sertic's corner and shoot from close range, the keeper getting a vital touch to send the ball over the bar.
The Magpies keeper then had to get down well to keep out Bellion's fizzing 18th-minute shot on the turn with Diabate failing to make the most of the rebound. But with 29 minutes gone Bellion and Ben Khalfallah combined down the left for the latter to curl in an inviting cross. Diabate gave Williamson the slip to power a firm header past Elliot.
Three minutes before the break Sammy Ameobi raced from his own half and played the ball into the path of older brother Shola, who fed it inside to Ranger, but he failed to collect the ball and the attack was over.
The younger Ameobi's departure at the break saw Vurnon Anita step into a reshaped midfield with Ranger and Shola Ameobi in attack, and the change almost paid dividends within two minutes when the latter got to his strike partner's knockdown ahead of keeper Kevin Olimpa, but could only poke wide.
Diabate sliced well wide under pressure from Williamson and Sertic only just missed from distance as the home side responded, but hopes of a fightback were dashed with 18 minutes remaining when Diabate ran on to Andre Poko's ball over the top and beat Elliot to wrap up the win.