The 33-year-old was closing in on Kenny Dalglish's record of playing 43 consecutive games for Scotland, but now looks certain to be denied that honour, five matches short.
After playing in Scotland's previous 38 games, Boyd's omission is expected to be formally confirmed tomorrow when the national squad meet at Hampden Park for their first training session.
Boyd, recently dropped at club level by the Celtic coach, John Barnes, has been suffering with a back problem for the past fortnight and has been told he needs a longer lay-off.
The Scotland manager, Craig Brown, said: "This is a real blow for us and Tom because I know he was looking at the record. Tom will have to take a couple of weeks complete rest."
His Parkhead colleague Paul Lambert is also set to pull out of the reckoning after making a slow recovery from jarring his knee against Dundee at Dens Park earlier this month.
There is also a question mark over Barry Ferguson's availability, as the Rangers midfielder's girlfriend Margaret is expecting a baby a week on Wednesday - the same date that Scotland clash with Estonia.
Brown may opt for Celtic's Jackie McNamara after the midfielder's impressive first club start of the campaign as Hearts were beaten 4-0 yesterday.
McNamara's ability to play in defence as well as further upfield, could seal his place as both Leicester's Matt Elliott and Blackburn's Callum Davidson are suspended at the weekend.
The Czech Republic have already qualified for the Low Countries from Group Nine, so Scotland's only hope of making the Euro 2000 is via the play-offs, but as Brown stresses their fate is still in their own hands.
They stand in second place, level on points with Bosnia who they meet in Sarajevo on Saturday, in the first of two vital meetings, the second being at Ibrox on 5 October.
Brown said: "A lot depends on the two games we still have to play against Bosnia. If we were to win on Saturday and again in Tallin against Estonia we would just about be in an unassailable position."
Sebastian Deisler of Hertha Berlin's has reportedly been forced to pull out of the German squad to face Northern Ireland in the European Championship qualifier on 8 September because of injury.
Deisler tore a thigh muscle in the 1-1 draw with Werder Bremen and is expected to miss at least three weeks.
Deisler, who arrived in Berlin this summer from relegated Borussia Moenchengladbach, is now in doubt for the Champions League clash with Chelsea on 21 September.Reuse content