Dortmund have climbed up to third in the Bundesliga after a rocky start and drew 1-1 at Manchester City in their Champions League Group D match on Wednesday with the hosts needing a 90th minute penalty to level.
Their high-tempo game against the English champions also silenced critics at home who said they were only a domestic force.
"It is the most difficult group in the Champions League, that is clear, but we have developed," Watzke told Reuters in an interview on Friday two days after his team moved up to four points from two games, as many as in the entire group stage last season.
"I did not understand the comments last year that we cannot play in the Champions League. We needed experience. We wanted these players last year to gather this experience themselves.
"We did not want to go out and buy three players and buy that experience and we see this year the team has been already successful. But obviously that does not mean that we will necessarily advance in the competition."
Watzke, who helped turn their fate around after joining in 2005, transforming it from a club on the brink of bankruptcy to one of Germany's most successful brands over the past two seasons, was equally modest about their domestic title chances.
Rivals Bayern are seven points ahead after winning all six of their league matches.
"I always talk about them with respect. Bayern are favourites to win the Bundesliga because financially they are in pole position having invested 70 million euros," said the 53-year-old manager.
"They have thrown everything into the pot to get the Bundesliga title back to Munich."
Bayern paid 40 million euros for Spain midfielder Javi Martinez, while also signing strikers Mario Mandzukic and Claudio Pizarro as well as Swiss international Xherdan Shaqiri.
"For us our top aim is to qualify again for the Champions League because this would mean we can further develop," said Watzke.
"The titles are the cherries on top of good seasons and it is great if they come but we are not that presumptuous to think that we will win a title every year."
Dortmund have so far lost just one of nine games in all competitions, a 3-2 defeat at Hamburg SV in late September that snapped their 31-match unbeaten run in the league.
"We knew it would be a bit tricky with nine of our players returning from Euro 2012 later than the others. But we are doing well in the two cup competitions and the league. We are absolutely on track."
Dortmund have every right to dream big these days with the club having posted a 34 million euro profit after tax with a turnover at 215 million for the 2011/12 fiscal year.
Watzke said profits this year would be less but turnover would continue to grow.
"The club on an operational level is now debt-free. We expect another strong result with figures again in the black. Obviously 34 million in profits after tax is a great performance.
"This fiscal year we will again be making a profit."
Watzke also ruled out bringing in big investors along the lines of Manchester City and Paris St Germain as financial independence was crucial for the club.
Earlier this week he had said he would "not even go to welcome" a sheikh or any other major outside investor.
"I said I would not receive him obviously not because we are not welcoming people but just because there would be no need.
"We want our freedom and independence, that is our culture and the culture of our 75,000 members. Being free and independent is German heritage.
"We have solved our financial problems and now we are strong, solid and we do not need it."