Centre-back McAuley, 37, has been ruled out of West Brom's Premier League opener against Bournemouth on Saturday because of a thigh injury.
Pulis said on Friday that McAuley "won't be fit for a couple of weeks".
Northern Ireland face San Marino away on 1 September before hosting the Czechs three days later.
"He's still struggling with his thigh so that's a problem for us," added the West Brom boss.
McAuley made his 72nd international appearance in the World Cup qualifier win in June but lasted only 23 minutes as he was forced off after suffering a recurrence of the thigh injury.
Up until his withdrawal in Baku, McAuley had played every minute of his nation's World Cup qualification campaign.
McAuley is unlikely to be the only significant absentee when O'Neill names his squad later this month.
Burton's Liam Boyce recently ruptured his anterior cruciate ligament, while Jamie Ward (calf) and Paddy McNair (knee) are unlikely to return in time.
Northern Ireland go into next month's games second in Group C and on course for a play-offs spot.
With four rounds of fixtures left, World champions Germany lead the table on a maximum 18 points with Northern Ireland five points off the place and the Czechs a further four points adrift in third spot.
West Brom manager Tony Pulis has said that Gareth McAuley will miss Northern Ireland's World Cup qualifiers against San Marino and the Czech Republic.