On a rainy evening in Bremen, the hosts struck either side of half-time through Hugo Almeida and inspirational Marko Marin to cancel out Tottenham's early advantage maintain their reputation as European comeback specialists.
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With William Gallas on the bench and Croatian Luka Modric not in Harry Redknapp's squad despite being declared fit to travel with the team, Tottenham looked to be in complete control when they added a second goal six minutes later.
With the home fans jeering their own players, Tottenham should have added a third through Bale's shot on the half hour but goalkeeper Tim Wiese was on hand to rescue Werder, badly missing key striker Claudio Pizarro
"We were so passive and we allowed everything to happen," said Bremen coach Thomas Schaaf. "We were not in the game early on and we just did not take the initiative."
With nerves getting the better of Tottenham's players, Germany international Marin quickly made amends for Arnautovic's miss with a fine solo effort at the edge of the box that left his marker frozen before releasing an unstoppable shot for the equaliser.
"We knew Bremen would be a team that would fight. But we were unlucky to concede that first Bremen goal late in the half," said Van der Vaart. "That turned things because we had really played a good first half."
