It was a superb effort from the home nation who will be left wondering about what might have been, with Kenny Miller hitting the woodwork and squandering another glorious chance in front of goal, after Scott Brown had also come close.
However, hopes of taking a point from this clash and keeping slim hopes of a play-off spot alive were dashed by a late strike from substitute Eljero Elia which maintained Holland's 100% record in Group Nine, while Norway defeated Macedonia to snatched the coveted runners-up spot on goal difference.
Scotland were dealt a blow before a ball had even been kicked with the news that first-choice goalkeeper Craig Gordon had failed to recover from a thigh strain in time, meaning a recall for David Marshall between the sticks, who produced his best performance in a dark blue jersey.
Steven Naismith made his first start, having played just eight minutes against the Faroe Islands previously, while Shaun Maloney filled the void left by the suspended James McFadden.
Paul Hartley was handed the role of anchor in midfield ahead of Graham Alexander, Steven Whittaker was given the nod at left-back in place of the injured Callum Davidson but Gary Caldwell, back from suspension, was forced to settle for a place on the bench.
Holland were also without their first choice goalkeeper, with rookie Michel Vorm - making his first competitive start - deputising for the injured Maarten Stekelenburg, although Wesley Sneijder was fit enough to start after picking up an ankle knock in the friendly against Japan.
There was a major let-off for the Scots with just four minutes on the clock when Dirk Kuyt unleashed a ferocious shot from the edge of the box which smacked off Marshall's left-hand post.
The early scare appeared to spark the home nation into action and Naismith teed up the shot for Rangers club-mate Kenny Miller but his effort cannoned off Andre Ooijer and nothing came of the resultant corner.
Scotland were threatening again moments later when Alan Hutton flighted a lovely ball to the back post but Scott Brown - the goal hero against Macedonia on Saturday - stabbed agonisingly wide of the upright as George Burley shook his head in disbelief in the dugout.
Darren Fletcher then recovered from a nasty challenge, which earned Robin van Persie a yellow card, to barge his way through a sea of orange shirts towards goal only to show too much to Vorm, who was able to smother before the Manchester United midfielder could unleash a shot.
Scotland had enjoyed a period of pressure without being able to capitalise and it was a full-stretch Marshall who was called into action to keep the scoreline level when he tipped a well-struck shot from Sneijder over the crossbar.
The Cardiff goalkeeper did well again moments later, this time blocking from Arjen Robben from 10 yards after he had been played through on goal by Robin van Persie.
With half an hour gone, it was Scotland's turn to be denied by the woodwork. Brown flicked into the path of Miller and he managed to shrug off Joris Mathijsen only to rifle off the crossbar with no-one able to follow up.
The Rangers striker then squandered another great chance to hand the Scots the lead. A long-range shot from Naismith was touched onto the post by Vorm, before Miller pounced on the rebound and fired straight into the arms of the goalkeeper when it looked so much easier to score.
The tempo had dipped slightly in the second half and it was Holland who went close when Sneijder's corner was met by the head of Kuyt but he nodded just over from close range.
Then, at a time when simulation has dominated the headlines, Liverpool man Kuyt was booked for diving by Danish referee Claus Bo Larsen after going to ground under pressure from McManus.
Still the Dutch pressed for the opener and Marshall came to the rescue with an excellent stop to prevent an angled drive from Robben finding the back of the net.
Miller had the opportunity to make amends for his earlier chances when the ball broke to him 10 yards out but once again he was denied by Vorm, who managed to block the point-blank shot for a corner.
Scotland continued to search for the elusive goal and every member of the Tartan Army was on their feet when Whittaker slotted into the path of Maloney who found himself one on one with the goalkeeper but failed to control properly and allowed Vorm to smother. A flag for offside went up, however Maloney appeared to be comfortably onside.
Maloney then turned provider with a long ball to substitute Kris Commons but he was off target with a diving header at the far post.
Instead, it was Holland substitute Elia who found the back of the net with eight minutes remaining when Weir inadvertently nodded the ball into his path and he sent an angled drive into the back of the net despite the efforts of Hutton on the line.