Yes, control theory has several applications in quantitative finance. Your strongest overlap would probably be in areas such as algorithmic trading, portfolio optimization, risk management, and optimal trade execution.
State-space models and Kalman filters can be used to estimate variables that cannot be directly observed, while system identification has similarities to estimating financial models from historical data. Optimal control and dynamic programming are also used for problems where a trader or portfolio manager must make a sequence of decisions while balancing return, risk, and transaction costs.
One important difference is that financial markets are much noisier and less stable than most physical control systems, so stochastic models are generally more useful than traditional deterministic transfer-function models.
For job searches, I would look at quantitative researcher, quantitative analyst, algorithmic trading, portfolio optimization, and optimal execution roles. Your control-systems background should be relevant, particularly if supplemented with probability, statistics, stochastic calculus, and programming.